Batshuayi came off the substitutes bench to tap in Marcos Alonso's low cross deep into stoppage time and settle a match looking destined to finish in a 1-1 draw.
Antoine Griezmann and Alvaro Morata had both scored previously to create a stalemate. Griezmann opened the scoring from the penalty spot against the run of play in the first half, after Chelsea centre-back David Luiz tangled with Lucas Hernandez in the box.
Yet Morata pegged Los Rojiblancos back after the break when he headed in a cross from Eden Hazard, who was superb on the night, before Batshuayi's dramatic late heroics.
Chelsea dropped had Pedro and Willian on the bench, while Cesc Fabregas played behind Hazard and Morata, per the competition's official Twitter account:
Atletico included Thomas Partey in midfield, while Angel Correa joined Griezmann in attack:
Los Rojiblancos had a vociferous crowd behind them, but Chelsea settled quicker. It was Hazard who led the charge, routinely running at the Atleti defence with pace and trickery, before crashing a shot off the inside of the post on 12 minutes.
Hazard had earlier been involved in twice teeing up Morata, only for the striker to drag his efforts wide. Even so, it was a bright and confident start from Chelsea, who had even succeeded in quieting the home support somewhat.
The Blues went close again 10 minutes later when Luiz chipped an astute pass toward Morata. His header was tipped over by Atletico goalkeeper Jan Oblak, who reacted quickly.
Oblak had saved, but the chance was further proof of Chelsea's growing comfort. The visitors' confidence was palpable when a nifty combination involving Fabregas, Kante and Hazard, ended with the latter drawing Oblak into another decent save.
Hazard's varied movement between the midfield and forward lines was causing Atleti a host of problems. He was ghosting on to either flank, as well as routinely drifting through the middle, where Partey was struggling to keep up.
Yet, for all of Hazard and Chelsea's initial dominance, Atletico should have been one up 10 minutes before the break. Raiding right-back Juanfran was released on the overlap and his smart cross nearly picked out Griezmann making a run to the near post.
The penalty incident came barely minutes later when Luiz was caught with a handful of Hernandez's shirt. Griezmann proved typically unerring from the spot.
The Frenchman has taken brilliantly to life in Atletico's new home, per Squawka Football:
Chelsea could have pegged Atletic back immediately had Alonso's shot not been deflected narrowly wide with Oblak beaten. Gary Cahill also saw a fine shot deflected away from goal.
Those misses looked sure to be punished when Saul Niguez and Koke combined brilliantly, with the latter's shot parried out by Thibaut Courtois. Unfortunately, Saul swiped the rebound a whisker wide of the post and Chelsea were still in it at the break.
Just as they had in the first half, the Blues started the second on the front foot. Cesar Azpilicueta drifted a cross barely inches out of the reach of Morata, before Moses dragged a shot wide.
Chelsea got the goal they merited a minute before the hour mark when Hazard's cross was met by a deft header from Morata. The equaliser earned Morata a moment of history:
It should have been 2-1 Chelsea moments later, but Fabregas scuffed wide when presented with an open goal.
Atleti boss Diego Simeone responded by substituting Yannick Ferreira Carrasco for former Chelsea striker Fernando Torres. Yet it was Morata who should have scored again when he raced clear only to toe-poke wide with Oblak already going to ground.
Batshuayi and Willian replaced Morata and Hazard with nine minutes to go, as Chelsea appeared content to settle for a creditable away point. A point was all either side appeared destined to earn until Alonso's low cross was swept in by Batshuayi.
Conceding for a second time in the same game is a rare occurrence for Atleti in this competition, per WhoScored.com:
Overall, the Blues did enough to merit snatching all three points at the death. Hazard and Morata were devastating as a double act up top, while Fabregas helped control possession in midfield.
This is a win sure to serve notice about Chelsea's ability to win this competition on Conte's watch.