The result was overshadowed by events at AEK Athens's match against Panthrakikos, however, in which AEK fans invaded the pitch after their relegation-threatened side conceded a late own-goal.
The match was subsequently abandoned with AEK set to face a disciplinary committee next week.
In the Athens derby, an astonishing difference of 37 points separated the two famous Super League rivals ahead of kic-off, but that did not show as Panathinaikos put in an impressive display at the Georgios Karaiskakis Stadium.
The Greens, who are on to their fourth coach this season in Giannis Vonortas in what has been a woeful campaign, deservedly took the lead in the 73rd-minute when Argentine striker Luciano Figueroa volleyed in Zeca's right-wing cross.
Olympiakos Pireaus, who wrapped up the title with six games to spare last month, rallied though and leveled matters three minutes from full-time when Mitroglou turned in Rafik Djebbour's attempted shot from close range.
It was a disappointing end to what had been a promising evening for Panathinaikos, who now miss out on a top five spot and the end of season playoffs which decide Greece's second Champions League spot and Europa League representatives.
At the Athens Olympic Stadium, AEK fell behind in the 87th minute when home defender Mavroudis Bougaidis turned the ball past his own goalkeeper from a Dimitris Papadopoulos cross, prompting the mass pitch invasion.
Both sets of players ran for the dressing rooms as play was stopped by referee Stavros Tritsonis and after a 90-minute delay the match was abandoned.
The game had already been halted once following a smaller-scale pitch invasion as AEK fans became impatient with the efforts of their team, who were just one point above the relegation zone before kickoff.
Wins for the other teams in relegation danger, Aris Salonika, who defeated Asteras Tripolis 5-1, and Veria, who were 5-0 victors against Platanias, meant that AEK face a tough task to avoid relegation for the first time in their history.