Dortmund boss Peter Stoger left Aubameyang out of the squad for the 1-1 draw with Hertha Berlin on Friday, claiming that his mind was elsewhere.
According to reports, that assessment was correct, with the 28-year-old keen on sealing a switch to the Emirates.
English news outlet 'Sky Sports' reports that Dortmund have already starting considering potential replacements for their star man, with Sampdoria's Duvan Zapata a key target.
Zapata is enjoying a solid season in Serie A, with six goals and three assists to his name in 15 league games this campaign.
The Colombian international, one of the players to watch at this year's World Cup, has previously been of interest to Dortmund, way back in 2013 when playing for Estudiantes in Argentina.
However, Dortmund are likely to face a battle to sign the 26-year-old, with Atletico Madrid reportedly interested in bringing the player to the Spanish capital.