Barton, who has a lengthy rap sheet during his career as a player and manager, has been sanctioned for his behaviour following his side’s 2-1 Sky Bet League One defeat by Sheffield Wednesday in April.
He was unhappy when Rovers had a goal disallowed for offside and was sent to the stands before continuing his protestations after the game.
An independent panel has fined him £3,000 and banned him from entering the stadium for Rovers’ first three games next season.
An FA statement said: “Joey Barton has been given a three-match ground ban and £3,000 fine for the three misconduct breaches that took place after Bristol Rovers’s game against Sheffield Wednesdsay in League One on Tuesday, April 18.
“The manager admitted that his behaviour after being sent off was improper and that he subsequently used abusive, insulting, and improper words towards a match official in both the tunnel and match officials’ changing room.
“An independent regulatory commission imposed his sanctions following a hearing and its written reasons will be published in due course. The three-match ground ban will apply to first-team competitive fixtures next season.”
Barton, 40, took over at the Memorial Stadium in February 2021 and, after winning promotion from League Two in 2021-22, guided Rovers to 17th place this season.
Rovers, managed by former Manchester City and Newcastle United midfielder Joey Barton, headed into Saturday's matches fourth in the table, behind third-placed Northampton – in the final automatic promotion place – on goal difference.
Northampton appeared to have done enough to secure a spot in League One as they won 3-1 at Barrow, only for events at the Memorial Stadium to halt their celebrations.
That scoreline at Barrow – unchanged from the 45th minute onwards – meant Rovers needed to win 7-0 against already-relegated Scunthorpe United to pip Northampton on goals scored.
Leading 2-0 at half-time, Aaron Collins and Antony Evans each scored twice against a much-changed Scunthorpe side before Elliot Anderson – on loan from Newcastle – added to his two assists with the decisive seventh five minutes from time.
That goal – the 19-year-old's seventh of a sensational loan spell, to go with six assists – prompted a pitch invasion that brought the game to a standstill.
As Northampton got word of the change in circumstances and chased a fourth goal, succeeding only in having goalkeeper Liam Roberts sent off, Barton and Rovers owner Wael al-Qadi pleaded with fans to stay off the pitch, having been warned the match could be abandoned.
Eventually, play resumed and Rovers held on for their joint-record margin of victory and a scarcely believable promotion to the third tier.
Barton praised Brown after his 20-yard goal late on completed a good night’s work for the summer signing from Exeter, who put the Gas on course for victory when he crossed for Luke McCormick to head the hosts into a 25-minute lead.
Vale defender Jesse Debrah was sent off after 38 minutes for a second bookable offence before right-back Jack Hunt popped up in first-half stoppage-time to double the lead and then Brown capped a fine personal show in style, four minutes from time.
Barton said: “Jevani’s a quality operator and that goal was important because it will lift a weight off his shoulders and I’m sure that he’ll now go from strength to strength for us.
“It was his best performance in the blue and white quarters and a lovely top-binner like that right in front of our most vociferous fans will certainly settle him and endear him to the supporters.
“It was a hell of a ball in for the first goal and everyone in the stadium now knows what a top-notch operator JB is.”
Barton says he is confident Brown will turn Rovers into a formidable attacking force.
He added: “JB’s had to be patient because it takes bit of time to get up to speed but tonight we looked unplayable up front with JB, Aaron Collins and Chris Martin and their pace and link-up play.
“I always knew his goal would come and I’m buzzing for him. We’re lucky to have him at our club. We have had to be streetwise to beat the rat race for him.
“But I know he’ll bear fruit over the next few months amid all the challenges we face this season.”
Vale boss Andy Crosby tipped former Halifax defender Debrah to learn from his sending off.
Crosby said: “Jesse is going to be fantastic for our club. He’s got fantastic attributes and we’ll be there to support him. He’ll learn from this and we’ll back him.”
“The referee has made a decision but I’m not sure (over) the first one, which looked like just a coming-together from the bench.
“As soon as you go down to 10 men, it’s going to be extremely difficult but the referee had a decision to make, the rules have changed in terms of how tackles are interpreted. It was a cheap one.”
Crosby praised his side for their show of resilience in the second half.
Crosby added: “We beat their press numerous times and got into their final third many times but if you don’t track your men into your own box and concede poor goals, you give yourself a big mountain to climb.
“We freshened things up at half-time with four changes to stay in the game and I’m so proud of the players’ reaction because they kept fighting and didn’t go under. We hung in there and defeat is difficult to take.”
