The home side were keen to make a fast start in their quest to secure Champions League football for next season, and they were able to do exactly that as with only 23 seconds on the clock.
Eintracht hit the front when the ball found its way to Rasmus Kristensen, who shot across goal and into the left corner to give his side a dream start.
However, their lead would only last three minutes, with the visitors drawing themselves level in style as the ball was pulled back to Manolis Saliakas on the right side of the area, allowing the right-back to produce a sumptuous first-time effort that flew over Kevin Trapp and into the net.
Despite having gone close to regaining the advantage, Frankfurt found themselves behind on the quarter-hour mark.
A long kick upfield from Ben Voll found Morgan Guilavogui, who enjoyed a slice of fortune to enable him to go around Trapp before rolling the ball into an empty net to give the away side a half-time lead.
St. Pauli came into the game with their top-flight survival still not secured, however, they were producing an impressive performance against the Champions League chasers, who were looking short of ideas.
Hugo Ekitike had registered six goal contributions (G3, A3) across his past six appearances, but the striker could only direct his header from inside the area straight into the gloves of Voll as the Kiezkicker continued to keep the hosts at bay.
Having applied relentless pressure throughout the second half, Die Adler eventually equalised with 19 minutes remaining when Fares Chaibi’s pass into the area found Michy Batshuayi, who took a touch before firing past Voll to set up a grandstand finish.
Batshuayi thought he had won the game for his side late on, but the striker was adjudged to have handled the ball just before poking it home from close range as the two sides settled for a point apiece.
Frankfurt remain third, knowing a point from their final game will be enough to secure Champions League qualification.
St. Pauli, meanwhile, can look forward to another top-flight campaign as they sit three points above the relegation play-off spot with a far superior goal difference.
Flashscore Man of the Match: Hugo Larsson (Eintracht Frankfurt)