The 27-year-old, who has hinted he may leave Dortmund at the end of the season, netted his 24th goal in as many Bundesliga games this season to put Dortmund 1-0 up on 53 minutes in Gelsenkirchen in the 150th Ruhr derby.
The Gabon international was thrown a black-and-orange wrestling-style mask from the sidelines as he ran to celebrate with team-mates after scoring for the fifth time in eight games against Schalke.
It was not the first time he has donned an elaborate mask to commemorate hitting the net against the Royal Blues.
In February 2015, Dortmund's self-styled 'Batman' wore a caped crusader mask, like that of the fictional superhero, after netting in that year's Ruhr derby.
On that occasion Germany winger Marco Reus joined in the fun by wearing a Robin mask as they both scored in a 3-0 home win.
Aubameyang's goal on Saturday left him level with Bayern Munich's Robert Lewandowski in the battle to be this season's top scorer in Germany.
Both players have each scored 24 league goals this campaign.
However, Dortmund's hopes of an away win to go third in Germany's top flight were dashed when Thilo Kehrer, 20, slotted home his first Bundesliga goal in only his 12th game to the delight of Schalke fans.
The hosts were then denied a penalty in the dying stages when the ball struck Dortmund defender Marc Bartra's hands.
The decision so incensed Markus Weinzierl that the Schalke coach was sent to the stands as the draw left Dortmund fourth in the table with Schalke ninth.