Serhou Guirassy headed home in the 83rd minute at the far right post as Dortmund rebounded on Friday night from a 2-1 defeat at Union Berlin in their previous match before the international break.
Ramy Bensebaini gave the hosts a 43rd minute lead with a looping header before St. Pauli grabbed an equaliser from Eric Smith's long range drive into the top left corner in the 78th.
Dortmund had more possession and several more chances, most notably from a Julian Brandt header on the stroke of halftime. But they were also lucky when the visitors had a goal from Morgan Guilavegui after half an hour disallowed upon review because he was ruled offside.
Socceroos captain Jackson Irvine played a full game for St. Pauli, who suffered their fifth loss in seven games since returning to the top flight.
"We are happy and relieved," Brandt told streaming portal DAZN.
"It wasn't easy. It was quite dour in the first half and we were a bit lucky with the offside goal. But we also had our chances and could have avoided the nervy finale if we had scored another."
Victory came ahead of next week's Champions League trip to Real Madrid, in what will be a rematch of last season's final the record winners from Spain won 2-0.
Dortmund (13 points) rose to fourth in the standings, one point behind leaders Bayern Munich and RB Leipzig. Promoted St. Pauli (four) remain third bottom.
With AAP.
16°C