Giuliano Simeone had put fourth-placed Atletico ahead at the Metropolitano on Saturday, but Marcus Rashford soon equalised before Nico Gonzalez was sent off ahead of the break.
Gerard Martin then had a red card early in the second half controversially overturned and substitute Robert Lewandowski struck the winner with three minutes left.
A sixth straight league win for Barca leaves them seven points clear at the top.
Relegation-battlers Mallorca had earlier stunned Real Madrid as a stoppage-time goal from Vedat Muriqi secured a 2-1 win at Son Moix.
Manu Morlanes fired the hosts in front against the run of play just before half-time, but a late header from Brazilian defender Eder Militao looked to have secured Real a draw, only for Kosovo forward Muriqi to snatch all three points.
Real Sociedad beat Levante 2-0 and it finished goalless between Real Betis and Espanyol.
Bundesliga leaders Bayern Munich came from behind to score twice in stoppage time and win 3-2 at Freiburg.
Bayern – without injured England captain Harry Kane – appeared set for just their second league defeat of the season after second-half goals from Johan Manzambi and Lucas Holer.
But Tom Bischof scored his first goal for Bayern in the closing stages and then fired home from outside the penalty area in the second minute of added time before teenager Lennart Karl turned home a dramatic winner.
Borussia Dortmund also left it late to win 2-0 at Stuttgart, with both goals from Julian Brandt and Karim Adeyemi coming in stoppage time.
There was no such drama as RB Leipzig won 2-0 at Werder Bremen to move above Stuttgart into third place.
Hoffenheim saw their European ambitions dented with a 2-1 home defeat by Mainz, with Phillip Tietz scoring twice.
Alejandro Grimaldo also hit a brace as Bayer Leverkusen came from behind to beat Wolfsburg 6-3 at the BayArena.
Augsburg drew 1-1 at Hamburg, who finished with 10 men, while it finished 2-2 between Borussia Monchengladbach and Heidenheim at the Westfalenstadion.
In Serie A, Fiorentina continued their climb away from the relegation zone with a 1-0 win at strugglers Verona.
Nicolo Fagioli scored with eight minutes left before Fiorentina forward Albert Gudmundsson was sent off and Verona substitute Tomas Suslov was also shown a late red card.
Lazio saw their three-matching winning run end after being held to a 1-1 draw at home by Parma and Sassuolo beat Cagliari 2-1.
In Ligue 1, Lens missed the chance to make up ground on leaders Paris St Germain after they slipped to a 3-0 defeat at third-placed Lille.
Rennes won 4-3 at Brest, with Esteban Lepaul scoring twice, to keep themselves in the mix for the European places and Strasbourg beat strugglers Nice 3-1 at Stade de la Meinau.
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