Halftime substitute Gignac, who returned from six weeks out with a broken foot on Wednesday, bent a powerful shot into the top corner in the 68th minute.
It lifted Marseille to 35 points from 18 games, with Lyon top on goal difference before their clash on Sunday at third-placed Paris St Germain, who have 32 points.
Toulouse were reduced to 10 men after 28 minutes when Cheikh M'Bengue was sent off, and 10 became nine on the stroke of half-time when Franck Tabanou was dismissed.
The visitors struggled to capitalise on their numerical advantage, as Toulouse's goalkeeper Ali Ahamada produced a fine display that included saving Andre Ayew's penalty kick in the 40th minute.
(Reporting by Gregory Blachier, editing by Stephen Wood)