André Schürrle gave Dortmund a narrow first half lead, only for Josip Ilicic to strike twice in five minutes to put his side in front.
Batshuayi levelled again on the night with an excellent strike, before scoring the winner in stoppage time, with Mario Götze setting up both goals.
Schürrle goal marks impressive first half
Dortmund were hoping for a good campaign in the competition as a disastrous showing in the UEFA Champions League, when they picked up just two points. They made two changes from their win against Hamburger SV in the Bundesliga, with Sokratis and Gonzalo Castro replacing the ineligible Manual Akanji and injured Shinji Kagawa. Atalanta, who topped a tough Europa League group, were able to recall both Mattia Caldara and Papu Gómeza following back problems with Remo Freuler also in from their 1-1 draw against Crotone on Saturday.
Both sides started well, with chances at both ends. For Dortmund, Marco Reus went just wide after he was found by Schürrle, who also had a shot of his own deflect wide. Batshuayi and Schürrle again had shots saved by Etrit Berisha. At the other end, Bryan Cristante’s shot was blocked by Sokratis and from the resulting corner, Caldara came inches from heading towards goal.
Schürrle had been Dortmund’s best player and deserved to give them the lead. Batshuayi won the ball up the field to launch a counter attack. Lukasz Piszczek picked up the ball from him, finding Schürrle with his cross. His first touch might have been a little heavy but he didn’t let it get away, cleverly scoring with his second.
Atalanta remained bright but Dortmund were dealing well with what threat they had to offer. There was only one more chance for either side before the break, and unsurprisingly it fell to Schürrle. His shot was straight at Berisha however.
Atalanta stun hosts before Batshuayi brace
The Italian visitors started the second half brightly again and they were soon back on level terms. Leonardo Spinazzola whipped the ball into the box, with Jeremy Toljan hesitantly trying and failing to head clear. That left Ilicic free to turn the ball into the net, despite a difficult angle on the right.
Dortmund looked like they had hit the self-destruct button, not for the first time this season, when they soon went behind. Cristante, from the left, was able to waltz through the centre of Dortmund’s defence, with his shot saved by Roman Bürki. It was typical of the Swiss goalkeeper’s campaign that he could only parry the shot to Ilicic, who gratefully accepted the invitation to score.
Peter Stöger threw on Götze in response, with Reus having played only his second match of the season here. The substitute would soon set up the equaliser for Batshuayi, although again it came from an Atalanta mistake as Rafael Tolói gave the ball away. Batshuayi, playing just his third game for Dortmund, struck hard and powerfully to beat Berisha.
It remained an open contest. Dortmund perhaps had the run of play, and nearly regained the lead a minute after coming level. Chrstian Pulisic’s effort was saved by Berisha, but it rebounded off Freuler and they were likely the ball went outside of the box. Freuler himself put a shot over, whilst a shot from defender Andrea Masiello was saved by Bürki.
It looked like the tie was set to go to Italy all square, albeit with Atalanta having the away goal’s advantage, but there was a late twist in stoppage time. Batshuayi won the game for Dortmund, again set up by Götze who placed the ball back into the box, after Tolói’s attempted clearance, helping the Belgian to a fifth goal in three matches.