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Marseille soon started to dominate possession, but only Gignac forced Benoit Costil into action in the Rennes goal before half time.
The hosts looked dangerous at the start of the second half, and managed to break the deadlock just six minutes in when Gignac unleashed a low drive from the middle of the box.
Gignac fired in a second just after the hour mark after Rennes cleared a corner, only for the striker to find the net from 20 yards out.
The striker looked for a hat-trick as the match progressed, but drifted offisde while waiting for a cross from Dimitri Payet before firing wide from a Rod Fanni pass inside the final 10 minutes.
Ntep tried to get Rennes back into the tie late on but had his shot blocked, while Vincent Pajot headed straight into the hands of Mandanda late on.
The miss allowed the hosts to finish the match in emphatic style, as Romain Alessandrini curled the ball into the top corner from a stoppage-time free kick.
The result moves Marseille to the top of the table, while Rennes sit seventh.