The pair had been together for 11 years and have two children, aged nine and seven.
Amid recent speculation of growing disharmony, a widely released statement via Shakira's communication agency on Saturday confirmed the couple have split.
"We regret to confirm that we are parting ways," Shakira's statement read.
"For the well-being of our children, who are our highest priority, we ask that you respect their privacy. Thank you for your understanding."
Pique met Shakira in 2011 while appearing in her single 'Waka Waka', the official song for the 2010 World Cup, which the centre-back went on to win with Spain.
He has spent the past 14 years with Barcelona and has made over 600 appearances for the club, 40 of those coming in the 2021-22 campaign.
Where Saturday nights would normally consist of fixtures in Spain's top flight, the live action was restricted to performances on an internet stream.
A host of LaLiga stars - including Pique - addressed supporters, while musicians performed at the online festival.
Fans were encouraged to donate to the Banco Santander Foundation, where the money would be used to buy medical equipment to combat COVID-19.
There have been over 72,000 confirmed cases of the virus in Spain, with close to 6,000 deaths.
The total raised ticked past €625,000 as the festival ended, although donations would continue to be welcomed until Sunday afternoon.
Barca's Pique was the most high-profile star to address those watching, as he claimed players and supporters alike could be "invincible together".
"Without training, at home and trying to stay in shape, it is not easy," the World Cup winner said. "We will get through it between all of us.
"It is a difficult situation, but doing something like what LaLiga is doing makes us feel proud of the players and the fans.
"It is something unique that means any LaLiga fan is able to contribute their grain of sand. I am very happy to be able to participate in such an initiative.
"There is rivalry when we are on the field of play, but when people need us, we are united.
"There will be a cost, it is difficult, we will have difficult times. Others will suffer it in person, but we have to make it through together. We are all invincible together."
Messi and Barca returned to training on Friday, albeit via individual sessions due to the COVID-19 crisis, with the squad divided over three pitches to ensure social-distancing requirements are upheld.
Barca followed a similar routine on Saturday as LaLiga hopes to resume in mid-June, having suspended the 2019-20 campaign in March.
"I didn't have any contact with Messi on the pitch, I only spoke to him on my mobile phone," Barca defender Pique told Movistar's El Partidazo.
"I didn't see him train either, I just crossed him in the parking lot. All the footballers we train in different fields. I am with Sergi Roberto and [Sergio] Busquets in a field, but we are separated."
Defending champions Barca were two points clear of bitter rivals Real Madrid through 27 matches when the season was postponed.
Barca head coach Quique Setien has previously said it would be logical for the Spanish giants to receive the title if the season was incomplete – a view strongly opposed by Madrid goalkeeper Thibaut Courtois.
Pique, though, would prefer to finish the campaign, adding: "I understand LaLiga's interest in finishing the season because there's a lot at stake.
"Despite being leaders, it would be quite ugly to win that way.
"We've spent a lot of time out of action and we have to keep in mind we need to be well prepared to avoid the risk of injuries, a few days of training more wouldn't be bad."
"They've kept us very well informed; [LaLiga president] Javier Tebas has dedicated many hours to it," Pique continued.
"There are people who are scared and it's important that everyone follows the protocol to the finest detail. It's better training as a group but we have to adapt."
