Third-placed Lyon moved seven points behind leaders Lille, who won 1-0 at AS Nancy on Saturday to go four clear of defending champions Marseille with four games left.
Brazilian defender Cris grabbed the winner with a sweet strike six minutes from time after the hosts had surrendered a two-goal lead.
Argentine striker Lisandro Lopez netted a 25th minute opener from the penalty spot for Lyon after top referee Stephane Lannoy decided he was fouled by Marseille centre-back Souleymane Diawara.
Lannoy had already chalked off an 11th-minute Marseille goal when he wrongly adjudged Andre Ayew to have handled the ball when in fact it struck his chest before forward Loic Remy, returning from a three-game ban, beat Hugo Lloris.
Lyon extended their advantage on 69 minutes through Cesar Delgado after a counter-attack but Marseille hit back a minute later when Lucho Gonzalez turned in a low cross before Remy bagged an equaliser following a corner.
"It's difficult but if we had led 1-0 after 10 minutes who knows?" Marseille coach Didier Deschamps, whose side next welcome Stade Brest on Wednesday, told reporters.
"The referee saw what no one else saw. It could have put us in a perfect situation but he saw a hand, I know there wasn't one.
FINE SAVES
"It's not been settled tonight. There are still 12 points to play," he added.
Both sides had other chances in a high-quality encounter but goalkeepers Lloris and Steve Mandanda were in excellent form, making several fine saves.
Miralem Pjanic also scuffed just wide from a great position for Lyon, humbled 2-0 at mid-table Toulouse last weekend to put their third and final Champions League qualifying spot at risk.
The absorbing victory though was a boost for Lyon boss Claude Puel, whose future at the Stade Gerland is uncertain, but Lisandro going off with what looked like a serious thigh injury was less good news for the coach.
Valenciennes, fourth-from-bottom before kick-off, surged four points away from the drop zone with a 2-0 home win over fifth-placed Stade Rennes.
The defeat meant Rennes' dwindling hopes of a Champions League qualifying round berth now look over but they have a four-point cushion in a probable Europa League spot.
