Chelsea had the wide majority of chances in the first half, most notably Eden Hazard's deflected shot from distance striking the post
But Atletico went ahead against the run of play as David Luiz tugged down Lucas Hernandez while trying to defend a corner, and Antoine Griezmann scored from the resulting penalty in the 40th minute.
And it was nearly 2-0 before the break as Saul Niguez put a rebound inches wide after Thibaut Courtois could only parry Koke's long shot into the centre of the box.
However, Chelsea equalized in the minute when Morata got a touch with his head to turn in Eden Hazard's cross.
And just as it seemed they would settle for a point, Chelsea found a goal from an elaborate routine, as Tiemoue Bakayoko flicked the ball on to Marcos Alonso, and it fell to Batshuayi to net the winner.