The 28-year-old broke the deadlock early in the second half on Saturday, as he collected the ball following a weak punch from Benoit Costil before acrobatically turning home.
And the lead was doubled soon afterwards, when Gignac again took one touch from a clearance before directing a shot home, this time from the edge of the area.
Substitute Romain Alessandrini capped off a fine performance for Marcelo Bielsa's side with a delightful free-kick in injury time to wrap up a win that deposed Bordeaux from top spot and kept Marseille's early title challenge intact.
Meanwhile, at Stade Municipal, Toulouse and Caen played out a remarkable 3-3 draw.
Florian Raspentino opened the scoring for visitors Caen with just seven minutes gone before Wissam Ben Yedder levelled things from the spot.
The match suffered something of a lull from there, before bursting into life in the final 15 minutes as the two sides shared four goals.
Substitutes Lenny Nangis and Adrien Regattin both got on the scoresheet in the space of seven minutes - the latter from the penalty spot - to make it 2-2 before a stunning Jean Calve free-kick looked to have won it for Caen.
However, Toulouse were not to be denied a share of the spoils, and they earned a point when Pavle Ninkov diverted a superb throughball with a first-time finish three minutes from the end.
With the likes of Paris Saint-Germain, Lille and Saint-Etienne playing on Sunday, there was little other movement at the top of Ligue 1.
That allowed Nantes to sneak into fifth place as an Itay Schechter goal sandwiched by one in each net from Jordan Amavi saw Nice slump to a 2-1 defeat.
As a result, Nice were leapfrogged by Reims, who moved out of the relegation zone with a 1-0 win at Lorient thanks to Benjamin Moukandjo's 72nd-minute goal.
Elsewhere, Metz claimed a 3-1 victory at home to Bastia, with Guido Milan and Juan Falcon's second-half goals proving decisive after Floyd Ayite had brought Bastia level by cancelling out Sergey Krivets' 14th-minute opener.
