Gundogan missed the first-leg due to an injury and also sat out of the weekends Bundesliga fixture.
The Bundesliga Giants recorded a 3-0 at home against Spurs and look set for a comfortable passage to the quarter finals.
Aubamayang opened the scoring for the home side on 30 minutes and Reus scored a second half brace to wrap up a memorable victory for the home side.
Dortmund manager Thomas Tuchel also left Turkish intentional Nuri Sahin on the bench for last weeks clash.
Dutch newspaper De Telegraaf uploaded a photo of City chief Txixi Begiristain and Gundogan’s uncle and agent Ilhan Gundogan in Amsterdam.
The 25-year-old has six assists and three goals in 32 appearances for Dortmund this season.