The French team's resounding victory gives them a big psychological boost going into their showdown at Spartak Moscow in three weeks' time.
Both teams have six points from four games in Group F but Marseille have a goal difference of plus-5 compared to Spartak's minus-1.
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"We don't know what could happen after the Moscow game so it's good to have such a goal difference," Marseille coach Didier Deschamps told the Canal Plus TV channel.
Chelsea lead the group on 12 points but bottom club Zilina have yet to pick up a point.
France striker Gignac, without a goal for a month, netted twice before the break and once in the second half as Marseille completely outclassed a weak Zilina side to beat the previous record for an away win in the competition, 5-0 by a host of clubs.
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Argentine playmaker Lucho Gonzalez also helped himself to two second-half goals and Gabriel Heinze and Loic Remy completed the rout.
LIVELY START
Ligue 1 champions Marseille made a lively start and were rewarded in the 12th minute when Gignac deflected a Benoit Cheyrou free kick into the net for his first Champions League goal.
The visitors added a second after 21 minutes, Gignac collecting a defence-splitting pass from Charles Kabore to slot the ball past keeper Martin Dubravka.
Heinze put the result beyond doubt three minutes later by heading home from a Cheyrou corner.
A clinical finish by Remy nine minutes before the break made it 4-0 and Lucho joined the goal party after the interval.
Mathieu Valbuena chipped the ball to the far post for the Argentine to head home in the 52nd minute and Gignac then completed his treble with a header.
Lucho made it 7-0 when he powered into the box before firing past the helpless Dubravka in the 63rd.
"They were better than us in all areas," said Zilina coach Pavel Hapal.
"Marseille's players were faster, braver and produced better combinations. My guys seemed to lack courage."
