Marseille cut the gap to Ligue 1 leaders Lyon to a single point thanks to their late 2-1 win over Guingamp on Sunday.
Mario Lemina opened the scoring for in the 84th minute before Andre-Pierre Gignac added the hosts' second in the 89th.
Marseille looked to have wrapped up the game and even Claudio Beauvue's 92nd-minute penalty and the sending off of Rod Fanni was not enough to stop the Stade Velodrome side from claiming the three points.
OM moved clear of Paris Saint-Germain to sit second with 44 points after PSG had earlier moved level thanks to a 4-2 win over Evian.
David Luiz and Marco Veratti scored their first goals for PSG as the defending champions claimed another three points.
Despite trailing to an early goal from Cedric Barbosa, the hosts hit back through Luiz and Veratti to ensure PSG held the half-time advantage.
Evian levelled things up once more thanks to an own goal from Gregory van der Wiel, but Javier Pastore restored the capital club's lead before a late strike from Edison Cavani put the result beyond doubt.
In the other game, St Etienne failed to apply pressure to Marseille as they were held to a goalless draw against Rennes at the Stade de la Route de Lorient.