The result - Chelsea's first success on Atletico territory - leaves Antonio Conte's team at the top of Group C with six points, while Atletico remain winless and have work to do in their double-header with Qarabag FK.
Atletico began their first European match at their new Wanda Metropolitano on top but it did not take long for Chelsea to begin to make an impact through Eden Hazard and Morata.
The latter fired a shot wide of the far post after receiving Hazard's pass, before the Belgian lashed an effort into the side-netting after jinking inside onto his right foot.
Morata sent another attempt wide of the far post soon afterwards, before Hazard almost marked his first significant start of the campaign with a sensational strike from 25 yards, only to see the ball ricochet off the post with Jan Oblak beaten.
The tempo in Madrid finally began to drop but that did not stop Chelsea from dominating proceedings, with Morata forcing a terrific save out of Oblak with a header after meeting David Luiz's 50-yard pass.
However, with 10 minutes remaining of the first half, Atletico finally started to make an impression at the other end of the pitch, although the home side were gifted their opportunity to take the lead.
Luiz was correctly adjudged to have hauled down Lucas Hernandez at a corner and Griezmann made no mistake with the resulting spot kick, which was drilled down the centre of the goal.
Marcos Alonso almost scored an immediate equaliser for Chelsea, with his half-volley being deflected marginally wide, but the Blues were fortunate not to fall further behind in the last action of the opening period.
Soon after the restart, Saul headed wide from inside the penalty area but it was Chelsea who were soon back in the ascendancy and the Blues deservedly equalised just before the hour mark.
Hazard - who was a constant menace throughout the night - curled a cross towards the near post from the right flank, and Morata was able to get across the defender to glance a header into the far corner.
At this stage, Chelsea had created three times more shots than their hosts and with their next effort, the English outfit should have been ahead with Cesc Fabregas getting his feet muddled from just six yards out with the goal at his mercy.
It was not long before the introduction of Chelsea old boy Fernando Torres but up the other end, his ex-employers wasted yet another opening as Morata dinked wide from close range after running clear of Hernandez.
The final quarter-of-an-hour was fiercely contested but chances were few and far between, despite both clubs showing ambition to claim all three points.
However, a few seconds after the additional three minutes which had been signalled by the fourth official, Batshuayi was perfectly placed to convert Alonso's low pass from close range for his fifth goal of the campaign.
The goal was met by the full-time whistle from the referee, and Chelsea will now head into their next clash against Roma aware that victory would already move the club to the brink of qualification for the last 16.