Pedro Henrique capitalised on careless control from new boy Mapou Yanga Mbiwa to open the scoring for Rennes after seven minutes, snatching possession before beating Anthony Lopes with a fine right-foot effort.
Lyon, shorn of several players due to injury, levelled through Nabil Fekir five minutes later.
Overall, though, the hosts were lethargic and Rennes made it 2-1 in the 56th minute when Mehdi Zeffane raced into the box and his low shot gave Lopes no chance.
Lyon have four points from their opening three games while Rennes are on six.
Monaco, Champions League quarter-finalists last season, were held to a 1-1 draw at Toulouse.
The home side took the lead in the 22nd minute when Tongo Doumbia finished from close range after a quick free kick caught Monaco off guard.
Youngster Thomas Lemar equalised for the visitors in the 65th minute, shaking off the attentions of the Toulouse defence before hammering the ball past Mauro Goicoechea from outside the area.
Bastia ran out 3-0 winners against Guingamp while Angers beat Ajaccio 2-0. A Hatem Ben Arfa-inspired Nice defeated Caen 2-1 and Nantes overcame Stade de Reims 1-0.
Champions Paris St Germain, top of the table with nine points, won 1-0 at Montpellier on Friday.
(Writing by Ed Dove; Editing by Tony Jimenez)
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