And it looked as though his struggles were set to continue on Saturday as he was guilty of two more glaring misses after Sokratis Papastathopoulos had given the visitors an early lead.
But he ended his own personal drought 10 minutes into the second half, tapping home from three yards after stunning work from Marco Reus.
His second arrived with 20 minutes to play - another straightforward tap-in thanks to superb approach play involving Ousmane Dembele and Erik Durm.
The victory, Dortmund's 12th successive Bundesliga win over Freiburg, allowed Thomas Tuchel's side to cement their position in third with fourth-placed Hoffenheim three points behind before their trip to Schalke on Sunday.
Dortmund made three changes from last weekend's 3-0 win over Wolfsburg and it was two of those, Sokratis and Raphael Guerreiro, who combined to open the scoring in the 13th minute.
Sokratis looked to be offside as Guerreiro swung in a free-kick from the right, which the Greece defender met with a header planted inside the right-hand post.
Aubameyang missed his kick when presented with a gilt-edged chance five minutes later following good work from Gonzalo Castro and Guerreiro, the Gabonese then thumping a shot straight at Alexander Schwolow as Dortmund sought a second.
Freiburg somehow survived on the half-hour as Schwolow superbly denied Guerreiro before Aubameyang and the Portuguese both failed to get a telling touch in the frantic scramble that ensued.
The hosts were breached early after the restart, however, as Reus nutmegged Caglar Soyuncu down the left and squared for Aubameyang who could not miss an empty net.
Freiburg's first real threat to Dortmund's goal came through substitute Florian Niederlechner, who was thwarted at close quarters by Roman Burki in the 65th minute.
And the importance of that stop was underlined shortly afterwards as Dembele's slide-rule pass released Durm, who selflessly teed up Aubameyang for another simple tap-in.
Substitutes Andre Schurrle and Shinji Kagawa combined late on, only for the latter to head wastefully wide, but it mattered little as Dortmund cruised to a comfortable success.