Pakistan won the decisive third ODI by 28 runs at Centurion.
They set South Africa a target of 321 after Fakhar (101) followed up his memorable innings of 193 last time out – an ODI record score in a run chase – with another century.
Pakistan captain Babar scored a century at this venue in the first ODI and almost repeated the trick before falling for 94, while Hasan Ali smashed 32 from 11 balls as the tourists scored 320-7.
Janneman Malan (70), Kyle Verreynne (62) and Andile Phehlukwayo (54) ensured South Africa – who were playing without their Indian Premier League contingent – were competitive in their run chase.
But they were ultimately bowled out for 292 in the final over as Pakistan continued a fine ODI streak that has seen them lose only two of their last 12 matches.
It is only the second time in 10 attempts that Pakistan have defeated South Africa in a 50-over series, this win coming after their triumph on the 2013 tour.
The two teams now turn their attention to a four-match T20 series which begins on Saturday.
With an all-new seam attack due to the absence of the likes of IPL duo Kagiso Rabada and Anrich Nortje, South Africa struggled to make an impression with the ball.
Fakhar had nine fours and three sixes as he put on 112 with Imam-ul-Haq (57) and then 94 with Babar to leave the tourists at 206-2 by the time his 104-ball innings came to an end.
He was dismissed by Keshav Maharaj, the pick of the Proteas bowlers with figures of 3-45.
The Pakistan innings had a huge finish when Hasan fired four maximums off the bowling of JJ Smuts (1-67) in the penultimate over.
Babar remained until he fell on the final delivery, caught by Verreynne on the boundary as he sought a six that would have taken him to three figures.
South Africa were left needing 76 from the last seven overs with five wickets in hand.
But their hopes of a successful run chase ended when they lost both Verreynne and Phehlukwayo – who put on 108 for the sixth wicket – in the space of seven balls.
It meant defeat for new captain Temba Bavuma, who has been handed the job through to the 2023 Cricket World Cup, in his first series at the helm.
Batter Fakhar was selected on Friday, as leg spinner Qadir has not yet recovered from the hairline fracture on his right thumb that he suffered during the recent series defeat to England.
Qadir will be a travelling reserve along with Mohammad Haris and Shahnawaz Dahani.
Fakhar will arrive in Brisbane from London on Saturday along with fit-again paceman Shaheen Shah Afridi and will be available for selection in the warm-up matches against England next Monday and Afghanistan two days later.
The 31-year-old left-hander was out first ball in his last T20I appearance, a defeat to Sri Lanka in the Asia Cup final just over a month ago.
He has played for his country 71 times in the shortest format, scoring 1,349 runs at an average of 21.75.
Pakistan start their quest to win the World Cup by taking on arch-rivals India at the MCG on October 23.
Pakistan T20 World Cup squad:
Babar Azam (captain), Shadab Khan, Asif Ali, Fakhar Zaman, Haider Ali, Haris Rauf, Iftikhar Ahmed, Khushdil Shah, Mohammad Hasnain, Mohammad Nawaz, Mohammad Rizwan, Mohammad Wasim Jnr, Naseem Shah, Shaheen Shah Afridi, Shan Masood.
Batsman Fakhar was named in a 35-man squad for three Twenty20 Internationals and two Tests against the Black Caps.
The 30-year-old opener tested negative for coronavirus but is not deemed to be well enough to fly out of Lahore with his team-mates on Monday.
Pakistan doctor Sohail Saleem said: "Fakhar's covid test report was received on Saturday which came out negative but today he picked up fever.
"As soon as his condition was reported, he was isolated from the rest of the squad in the team hotel. We are constantly monitoring his condition and remain hopeful of his quick recovery; however he is not fit to travel with the squad and as such has been withdrawn from the touring party."
Pakistan and New Zealand start the T20 series at Eden Park on December 18.
The paceman has been out since July due to a knee ligament injury, but he completed his rehabilitation programme at Premier League football club Crystal Palace in London.
Afridi is available for Pakistan's World Cup warm-up games against England and Afghanistan next week.
The left-arm quick's fitness will be assessed prior to Pakistan's first game of the tournament versus fierce rivals India at the MCG on October 23.
Afridi said: "I am super-excited at the prospects of rejoining the national side for the T20 World Cup and playing my part in our Australia campaign. It has been a difficult period for me to be miles away from the game and the team I love the most, and not be part of some gruelling and exciting matches.
"I have been bowling six to eight overs trouble-free for the past 10 days with full run-up and pace. While I have enjoyed bowling and batting in the nets, nothing can replace the feel of the match environment and I can't wait to be in that setting.
"It has been a rigorous and challenging rehabilitation programme, but I have thoroughly enjoyed it. To be honest, I am feeling fitter than ever before and can't wait to wear the playing kit and fire a few thunderbolts.
"I want to thank the PCB medical advisory committee as well as Crystal Palace FC for allowing me to use their outstanding facilities and looking after me so well during the rehabilitation programme."
Opening batter Fakhar Zaman, one of three travelling reserves, will also fly to Brisbane this weekend to complete his rehabilitation after he was also sidelined by a knee injury.
The Black Caps took an unassailable 2-1 lead in the five-match T20I series, thanks in the main to Tim Robinson (51) and bowling duo William O'Rourke (3-27) and Ben Sears (2-27) on Thursday.
Set a target of 179 to win, Pakistan looked on their way to victory when Fakhar Zaman got going, but he was eventually dismissed on 61 by Sears.
Abbas took three wickets in New Zealand's innings, yet he could only contribute a single run to Pakistan's cause as the hosts fell just short in Lahore.
Data Debrief
Shadab Khan did not bowl a single delivery for Pakistan, which is the first time that has happened in a completed T20I innings.
He did take an exceptional catch to dismiss Mark Chapman, but it was not enough to inspire Pakistan.
They have 12 confirmed players for the 2024 season and will have five spots to fill at the draft in July.
The Falcons, who are replacing the Jamaica Tallawahs in this year’s tournament, will feature Pakistani internationals Mohammad Amir, Imad Wasim and Fakhar Zaman, all of whom are currently featuring in the T20 World Cup which is taking place in the Caribbean and USA.
Their overseas contingent will be rounded out by Australia’s Chris Green and Afghan all-rounder Azmatullah Omarzai.
Omarzai, currently representing Afghanistan at the T20 World Cup, recently took part in the Indian Premier League (IPL) for the first time with the Gujarat Titans.
Brandon King and Fabian Allen will also be part of the Falcons squad for 2024 as well as hugely exciting Antiguan batter Jewel Andrew who starred at the Under 19 World Cup earlier this year.
King previously represented the Guyana Amazon Warriors and the Jamaica Tallawahs, who he captained to the title in 2022, while Allen has previously represented the Patriots and Tallawahs.
The full list of signed players for the Falcons is as follows: Mohammad Amir, Imad Wasim, Fakhar Zaman, Brandon King, Jewell Andrew, Chris Green, Shamar Springer, Joshua James, Azmatullah Omarzai, Kelvin Pitman, Hayden Walsh Jr, Fabian Allen
Patriots captain Andre Fletcher called the coin correctly and elected to field first and South African pace merchant Anrich Nortje, who would play a crucial cameo with the bat later in the game, skittled Falcons opener Teddy Bishop for just 1. Fakhar Zaman then opened his muscular shoulders, hitting five fours and two sixes in making 43 off 32 balls with Kofi James ably supporting with a 22 off 24.
England’s Sam Billings was spectacularly caught on the boundary rope at deep midwicket, Odean Smith showcasing pristine footwork and clear thinking in juggling the catch to himself on the boundary edge.
The star of the Falcons innings though was 17-year-old Jewel Andrew, who showed maturity beyond his years and an eye-catching talent by striking 50 off just 30 balls to post a challenging target of 163-4 for the Patriots to chase.
An ebb and flow of runs and wickets followed as a dramatic match headed down to the final over and then the final delivery. Nortje held his nerve to get the single needed off Roshon Primus to give the Patriots a last gasp win, they equal their win tally of last year’s tournament after just one game.
Kyle Mayers was awarded Player of the Match for a crucial 39 off 24 balls from number three but when he was dismissed by Mohammad Amir in the 16th over it left the Patriots on 133-6 and with plenty still to do. Despite wickets falling steadily, including two in the final over, the Patriots lower order managed to get over the line and chalk up a win to kick off their campaign.
“I’m happy we won this game” Patriots captain Andre Fletcher reflected in the moments after victory. “I want us to be positive but at the same time, we have to be smart about it. Enjoy the cricket as much as possible, enjoy each other's success and stick together as a team. Once we do that, we have the personnel to do well.”
The 2024 CPL is up and running and the opening match well and truly whetted the appetite for the next five weeks of action.
The 34-year-old Sarfraz replaces Azam Khan for the upcoming tournament two years after he was sacked as captain.
Haider takes Mohammad Hasnain's spot, while fellow batter Fakhar comes into the 15-man squad at the expense of Khushdil Shah.
The selectors opted to tinker with the initial squad they named after keeping a close eye on performances in the National T20 Cup.
Sohaib Maqsood has retained his place after there were doubts over his participation due to a back injury.
The batter underwent an MRI scan this week but has been cleared to travel for the tournament in the United Arab Emirates and Oman.
Pakistan start their quest for T20 glory with a mouthwatering Group 2 clash against fierce rivals India at the Dubai International Cricket Stadium on October 24.
Pakistan squad:
Babar Azam (captain) Shadab Khan, Asif Ali, Fakhar Zaman, Haider Ali, Haris Rauf, Hasan Ali, Imad Wasim, Mohammad Hafeez, Mohammad Nawaz, Mohammad Rizwan, Mohammad Wasim, Sarfraz Ahmed, Shaheen Afridi, Sohaib Maqsood.
Babar Azam's century propelled Pakistan to a dramatic three-wicket win in the first match on Friday, but they fell short of winning the series at the Imperial Wanderers Stadium after some significant contributions at the top of the order from the hosts.
Captain Temba Bavuma was in supreme form, hitting a wonderful 92, while Quinton de Kock (80) and David Miller (50 off 27 balls) helped South Africa to 341.
Zaman's 155-ball 193 was the highest score in a chase in ODI history, although it was not enough to help his side to an improbable victory.
Aiden Markram set the tone for South Africa's innings with an impressive 39, ultimately falling to a Faheem Ashraf delivery.
De Kock and Bavuma anchored South Africa, putting up a 114-run partnership for the second wicket, the former bowled by Haris Rauf 20 runs shy of his century.
Rassie van der Dussen plundered 60 off 37 balls to put the hosts in a strong position, before Bavuma was caught by Azam from Rauf's bowling for 92.
Miller then gave South Africa's total an even healthier look with a half-century.
Pakistan suffered an early blow in the chase when Imam-ul-Haq was dismissed by Lungi Ngidi in the second over, while Anrich Nortje took three quick wickets.
The visitors' hopes of an unlikely win looked in tatters, but Zaman gave them hope with a record-breaking innings.
His spellbinding 193 surpassed Herchelle Gibbs' 175 as the highest individual score at the Imperial Wanderers Stadium, and was the second highest ever in a losing ODI cause.
Zaman fell in the penultimate over when he was run out by Markram after De Kock had cheekily encouraged him to think the ball was going to the other end.
