Aubameyang, who notched 22 league goals last season to emerge as the Premier League joint-top scorer, continued from where he stopped, opening the scoring in the 36th minute.
Dembele, who replaced Amine Gouiri at the start of the second half, levelled for his side in the 66th minute before completing his double 10 minutes later.
Aubameyang featured for 86 minutes in the encounter while Burkina Faso forward Bertrand Traore was replaced by Guinea international Boubacar Fofana.
Dembele, who bagged 15 league goals last term, will hope to continue with the impressive pre-season form when the 2019-20 season gets underway.
Arsenal will take on Angers and Lyon will square up with Liverpool in their next pre-season friendly games on Wednesday.