The target-man was included for Dortmund at home to Freiburg, his first Bundesliga appearance since December 16 having been dropped for Dortmund’s last two games.
He started as striker with English teenager Jadon Sancho, 17, on the left wing and US international Christian Pulisic, 19, on the right.
Dortmund have reportedly rejected a second bid by Arsenal of 58 million euros ($72m) with the German club thought to be holding out for 70 million euros for their top-scorer.
“We have a clear position,” said Dortmund’s director of sport Michael Zorc before kick-off.
“Our demands must be met and so far Arsenal’s attempts have not matched them.”
With the January transfer window to close at midnight (2300 GMT) on Wednesday, time is running out for the deal to be completed.
The Gunners want to sign a striker to replace Alexis Sanchez who joined Manchester United last week.
Aubameyang has scored 141 goals in 212 games for Dortmund in all competitions since his arrival in 2013.
Dortmund are seventh in the German league after drawing both of their last two games, goalless at home to Wolfsburg and 1-1 away to Hertha Berlin, without Aubameyang.
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