The Gabon international is at the centre of transfer talks between the two clubs, with the Rossoneri confirming this week that they are interested in signing him.
Aubameyang, also rumoured to be on the radar of Chelsea and Liverpool, put the uncertainty over his future to one side on Tuesday afternoon by bagging a goal in either half at the Tianhe Stadium in Guangzhou.
United States international Pulisic was involved again soon after, this time being brought down inside the area to win his side a penalty, which last season's Bundesliga top scorer Aubameyang converted.
A third goal of the match arrived 24 minutes in when Carlos Bacca was given plenty of time and space to fashion a shot from the edge of the box, superbly sending it past Roman Weidenfeller to halve the deficit.
The German club were seeing more of the ball as the first half continued, coming close to regaining their two-goal advantage through Gonzalo Castro, who sent a volley high over the bar after being spotted by Aubameyang from the right.
Dortmund did net a killer third shortly after the hour mark, however, as Castro powered forward on the counter and picked out Pulisic, with the youngster in turn setting up Aubameyang to earn the victory for BVB.
Sokratis Papastathopoulos produced a big block in the final 10 minutes to prevent Milan from pulling one back, meaning defeat for Europe's top spenders Milan in their first ICC match.