Substitute Batshuayi tapped home from close range with the last kick of the game from Marcos Alonso’s cross.
The Blues fell behind to a 40th-minute Antoine Griezmann penalty despite having the better of the first half when David Luiz needlessly pulled the shirt of Lucas Hernandez at a corner.
But Chelsea, who hit the post through Eden Hazard in the opening stages, again impressed after the interval and were rewarded when Alvaro Morata equalised with his fourth goal in five days.
The Spaniard deftly flicked Hazard’s accurate left-wing cross into the far corner for his first Champions League goal for Chelsea.
Batshuayi’s winner came after missed opportunities for Cesc Fabregas and Morata as Chelsea became the first English team to win away at Atletico and condemn them to defeat in their first European game at their new stadium.
It also ends an 11-game unbeaten run at home in Europe for Atletico, who have reached two Champions League finals in the past four seasons.
Victory means Chelsea stay top of Group C on six points, two clear of Roma and five ahead of third-placed Atletico.