Nice climbed to fourth on 29 points after 16-year-old Neal Maupay's stoppage-time goal secured a 3-2 home victory over Evian Thonon Gaillard.
It was the first league goal in six appearances for Maupay who came off the bench in the 86th minute.
Half-time substitute Gignac, who returned on Wednesday after six weeks out with a broken foot, bent a powerful shot into the top corner in the 68th minute to earn Marseille's seventh away victory of the season.
"It is a beautiful story for me," Gignac told reporters after sinking former team Toulouse who played the entire second half with nine men.
"It made it easier for us but they played with a lot of heart. Tonight luck was on our side."
The first Toulouse player to receive a red card was Cheikh M'Bengue when he produced a rough tackle on Morgan Amalfitano in the 28th minute.
PENALTY SAVED
Marseille won a penalty 13 minutes later when Franck Tabanou fouled Jordan Ayew but his older brother Andre Ayew's spot-kick was saved by Toulouse's outstanding keeper Ali Ahamada.
Ten men became nine for the home team when Tabanou was dismissed for a violent challenge on Rod Fanni on the stroke of half-time.
Marseille went close to scoring again when Ahamada saved Joey Barton's volley and a powerful effort from Lucas Mendes.
Gignac, who had replaced Amalfitano at half-time, then struck his sixth goal in 11 appearances.
Jonathan Zebina had the best chance to rescue a point for Toulouse but his header was saved by keeper Steve Mandanda in the 74th minute.
"We began well but then ruined it all," said Toulouse coach Alain Casanova referring to the two red cards.
Casanova's men have only won once in eight league games and occupy 12th spot on 23 points.
Argentine striker Dario Cvitanich scored his ninth and 10th league goals of the season to help Nice recover from going 2-0 down after early efforts from Evian pair Yannick Sagbo and Cedric Barbosa.
Elsewhere, Marco Estrada's spectacular 35-metre volley in the 14th minute set champions Montpellier on the path to a 4-0 home drubbing of Bastia.
Montpellier's fourth win in five games took them up to ninth on 26 points, level with Lille who drew 1-1 at promoted Stade Reims.
