However, the breakthrough would come just 11 minutes into the game as Papu Gomez's corner was flicked on at the near post by Mattia Caldara, where Rafael Toloi was on hand to steer the ball into an empty net.
Both sides delivered plenty of frantic attacking football in the first half as Andre Schurrle was denied by Etrit Berisha, Mario Gotze saw his goal chalked off for offside, and Sokratis Papastathopoulos was forced to make a last-ditch tackle on Gomez.
The second half saw Atalanta impose themselves on the game but their wastefulness repeatedly let Dortmund off the hook, with Gomez, Ilicic and Cristante all failing with their respective efforts in front of goal.
Gian Piero Gasperini's charges would come to rue their missed opportunities because, on 83 minutes, Schmelzer struck an equaliser on the rebound after Berisha spilled Marco Reus's initial shot in the wet conditions.
The shellshocked hosts were unable to find a late winner to force them over the line and the final whistle blew on Dortmund progressing to the last 16 of the competition by a slender margin.
ATALANTA BC (3-4-1-2): Berisha; Toloi (Cornelius 88'), Caldara, Masiello; Hateboer, De Roon (Petagna 87'), Freuler, Spinazzola; Cristante; Ilicic, Gomez
BORUSSIA DORTMUND (4-2-3-1): Burki; Toljan (Schmelzer 46'), Toprak, Papastathopoulos, Piszczek; Dahoud (Isak 81'), Sahin; Pulisic (Reus 59'), Gotze, Schurrle; Batshuayi