OM were looking to build on their midweek success over Bastia and were helped on their way by a Toulouse side who saw both Cheikh M'Bengue and Franck Tabanou sent off before the interval, while Andre Ayew also missed a penalty for the visitors.
However, Gignac's goal midway through the second half proved enough to earn Elie Baup's men the spoils and leave the hosts without a win in four league matches.
It was Toulouse who had the first chance after 25 minutes, with Tabanou's cross into the area resulting in a header for Pavel Ninkov which was swept off the line by defender Lucas Mendes.
However, things took a turn for the worse for the home side moments later when M'Bengue was given a straight red card for a dangerous tackle on Morgan Amalfitano.
Tabanou then went into the book after 39 minutes for a challenge on Jordan Ayew which resulted in a penalty being awarded to Marseille. However, Ayew's brother Andre saw his spot-kick saved by Ali Ahamada.
Toulouse's woe deepened before the interval when Tabanou was shown his second yellow card in five minutes for a poorly timed tackle on Rod Fanni.
But goalkeeper Ahamada again kept the scores level on the stroke of half-time with an agile save to keep out Joey Barton's powerful drive.
Marseille's attempts to go in front were once more halted by Ahamada early in the second half, with Mathieu Valbuena the latest to see an effort turned away by the home keeper.
But the visitors eventually made the breakthrough after 67 minutes thanks to Gignac, who made the most of a through-ball from Jordan Ayew before picking out the top-left corner.
Despite their obvious disadvantage, Toulouse fought on and came close to snatching a point six minutes later only for Steve Mandanda to deflect away a Jonathan Zebina header at full stretch.