Augsburg, however, fell behind after 32 minutes when Marius Wolf fouled Manolis Saliakas in the box. Sinani stepped up and confidently dispatched the penalty to give St. Pauli the lead.
But the home side restored parity nine minutes later when Claude-Maurice delivered a pinpoint corner to the near post, where Gregoritsch rose highest to head past Nikola Vasilj.
The Austrian striker then completed the turnaround in the 59th minute with a clinical finish after a perfect through ball from Claude-Maurice for his second assist of the match.
Thanks to the win, Augsburg opened up an eight-point gap to St. Pauli, occupying 17th place, which results in direct relegation to the 2. Bundesliga.