Gomis found the net for the visitors from the penalty spot after three minutes and converted his side's second effort on target in the 34th.
He added the fourth on 72 minutes, to take his personal tally to nine league goals, after Steed Malbranque had fired home with a superb volley three minutes into the second half.
Lyon - hammered 3-0 at Toulouse last weekend - have 28 points, two ahead of second-placed Paris Saint-Germain and Marseille in third.
"We were so frustrated a few days ago. It is such a pleasure playing in this team and to clinch top spot," goalkeeper Remi Vercoutre told French channel Canal+.
Midfielder Maxime Gonalons added: "We really enjoyed tonight and we have a lot more to come."
Loic Remy netted a goal for Marseille in the 77th but Rod Fanni's dismissal for a bad tackle on Mahamadou Dabo with 10 minutes remaining added to the host's woes.
Lyon needed only three minutes to show they had left their last defeat behind them.
Goalkeeper Steve Mandanda fouled Gomis as he ran onto Alexandre Lacazette's pass. The France striker picked himself up and buried the penalty.
Marseille pushed hard for an equaliser but Vercoutre saved their only clear-cut chance when he parried a powerful Jordan Ayew header in the 15th minute.
A well-organised Lyon doubled their lead when Gomis superbly controlled a Dabo cross and then skipped past Mandanda to score into an empty net.
Remy came off the bench for Joey Barton at the start of the second half for Marseille, who would have climbed to the top with a draw.
But Lyon effectively ended the contest within three minutes of the restart when Malbranque volleyed in a Lacazette cross.
Marseille laboured on a heavy pitch and never really threatened Vercoutre, exposing their goal to Lyon's quick counter-attacks.
They were eventually punished when Gomis fired home from Anthony Reveillere's pass.
Remy then took advantage of a confused situation to score his first league goal of the season in the 77th but Lyon were far too strong, with Gomis wasting a chance for a fourth goal of his own in stoppage time.
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