- The hosts took the lead after just 11 minutes through defender Rafael Toloi
Published: 22:00 GMT, 22 February 2018 | Updated: 22:00 GMT, 22 February 2018
The Bundesliga giants are one of the favourites to go all the way after finding themselves in this competition following their exit from the Champions League but threatened to come unstuck here at the first hurdle.
Rafael Toloi capatilised on some lazy Dortmund defending to stab home after just 11 minutes.
For much of the game it appeared that that was going to be enough for the Italian side to sneak through on away goals.
But Dortmund struck back through the unlikeliest of super subs. Marcel Schmelzer came on early in the second half and saved Peter Stoger's side by scoring with seven minutes to go.
Rafael Toloi slid in to open the scoring after just 11 minutes to make the score 3-3 on aggregate
The Atalanta players bundle Toloi to the ground as they celebrate taking the initiative
MATCH FACTS AND MATCH ZONE
Atalanta (3-5-2): Berisha; Toloi (Cornelius 88), Caldara, Masiello; Hateboer, Cristante, de Roon (Petagna 87), Freuler, Spinazzola; Ilicic, Gomez;
Subs not used: Palomino, Gosens, Castagne, Haas, Gollini
Goalscorers: Toloi (11)
Booked: Hateboer, Spinazzola
Borussia Dortmund (4-2-3-1): Burki; Piszczek, Papastathopoulos, Toprak, Toljan (Schmelzer 46); Dahoud (Isak 82), Sahin; Pulisic (Reus 59), Gotze, Schurrle; Batshuayi;
Subs not used: Weidenfeller, Zagadou, Beste, Castro
Goalscorers: Schmelzer (83)
Booked: Papastathopoulos, Piszczek, Buerki
Atalanta took the lead after 11 minutes with Rafael Toloi sliding in to convert a corner kick. CLICK HERE to see more from Sportsmail's brilliant MATCH ZONE feature.
Atalanta goalscorer Toloi dribbles the ball forward under pressure from Mario Gotze
Michy Batshuayi drives forward and looks to get past Atalanta defender Mattia Caldara
Josip Ilicic tries a speculative acrobatic effort but fails to connect with the ball in the first half
Ilicic demonstrates good strength to shrug off the challenge of Sokratis Papastathopoulos
Atalanta goalkeeper Etrit Berisha falls awkwardly after clashing with Dortmund's Gotze