Last season's runner-up Lyon had drawn and lost in the first two rounds, and Rennes piled on the misery at Stade de Gerland by scoring after just seven minutes through Pedro Henrique.
Nabil Fekir equalised for Lyon five minutes later but Mehdi Zeffane, who moved to Rennes this northern summer after 12 years at Les Gones, scored what proved to be the winner from close range on 56 minutes.
It means Lyon is now in 11th place, with Rennes moving up to fifth with its second win of the season.
Bastia moved back to within two points of table-topper Paris Saint-Germain thanks to a 3-0 win over Guingamp, with Julian Palmieri netting a double and Lassana Coulibaly adding the third late on.
Bastia is one of three teams on seven points after Angers and Nantes beat Gazelec Ajaccio and Reims respectively.
Angers skipper Cheikh Ndoye scored a first-half brace in a 2-0 victory, while Nantes kept a third straight clean sheet and saw Ermir Lenjani score the only goal of the game on 77 minutes.
Monaco had shared a goalless draw against Lille last time out, and it drew again, though it at least got on the scoresheet in a 1-1 finish against Toulouse, Thomas Lemar equalising for the principality side after Tongo Doumbia had struck for the host.
Caen suffered its first loss of the season, having won two before this weekend, as former Newcastle United man Hatem Ben Arfa scored for Nice in a 2-1 win, its first of the new campaign.
