The Argentinean played a one-two with Luis Suarez on the edge of the Atletico area before curling a left foot shot into the back of the Atletico net to decide an entertaining game that could have gone either way as rain poured down in Madrid on Sunday evening, reports Xinhua news agency.
Both sides had chances to win the game with Barca keeper Marc Andre Ter Stegen making two brilliant first half saves, while Gerard Pique, who had to leave the pitch with an injury in the closing minutes, saw a header bounce back off the crossbar.
Barcelona had been in danger of losing the leadership after Real Madrid dug deep to take all three points from their visit to Deportivo Alaves with goals from defenders Sergio Ramos and Dani Carvajal 24 hours earlier.
Ramos headed Madrid into a 52nd minute lead after a free kick taken by Tony Kroos but then committed a needless penalty against Joselu to allow Lucas Perez to equalise from the spot.
Carvajal sealed the points for Madrid from close range after Alaves keeper Fernando Pacheco had pushed Isco's header onto the post.
Sevilla remain third but had to work hard to beat Leganes with Diego Carlos scoring the only goal of the game in the 62nd minute against the bottom of the table side. Leganes have improved under coach Javier Aguirre, but are starting to get left behind in the battle to avoid relegation.
Athletic Club Bilbao opened the scoring in their 2-0 win at home to Granada with a twice-taken penalty from Raul Garcia.
Raul's first penalty was saved by Granada keeper Rui Silva, but he was adjudged to have moved off his line and the forward made no mistake with his second attempt. Yuri Berchiche secured the win for Athletic Club with a close range finish from Unai Garcia's pass in the closing minutes.
Real Sociedad produced a convincing display to beat local rivals Eibar 4-1 thanks to goals from Robin le Normand, Mikel Oyarzabal, Willian Jose and Martin Odegaard, who curled in an impressive 25 yard effort to conclude the scoring.
( With inputs from IANS )