Gignac, who had been left out of the Marseille starting XI by manager Elie Baup for their last four games in all competitions, was restored to the side after netting in the 2-1 win over Sochaux prior to the international break.
And it was a decision that proved crucial as the France international scored the visitors' second goal of the night in magnificent fashion.
Winger Dimitri Payet had opened the scoring for Marseille after 27 minutes, the former Lille man turning home Florian Thauvin's low right-wing cross with an emphatic finish.
Ajaccio levelled matters just four minutes later as Venezuelan defender Grenddy Perozo headed past Steve Mandanda from Johan Cavalli's free-kick.
But, Marseille regained the lead six minutes before the interval, Gignac finding the net with a spectacular volley into the top corner after he had shown great control to bring down Kassim Abdallah's cross.
From there Ajaccio were never able to re-establish a foothold in the game, and Marseille's victory was all but assured when Payet turned provider to set up Thauvin for a simple finish from point-blank range two minutes before the hour mark.
Marseille wasted further chances to increase their advantage in the latter stages of the second half, but it mattered not as they cruised home to secure a victory that does a great deal for their hopes of returning to the Champions League and plunges managerless Ajaccio further into the relegation mire.
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