Gourcuff debut spoiled by dad
Elsewhere, leaders Toulouse made it four wins in four games as midfielders Etienne Capoue and Franck Tabanou earned a 2-0 victory at Nancy.
Ten-man Caen suffered their first defeat of the season when they lost 2-0 at home to fellow promoted side Stade Brest.
Caen, who had midfielder Sambou Yatabare sent off early in the game, stayed on seven points, three more than Brest.
France playmaker Gourcuff, whose father Christian is Lorient's coach, came on as a first-half substitute with Lyon already 1-0 down thanks to a Kevin Gameiro penalty.
Lynel Kitambala then sealed Lorient's win after the break.
Lyon, who signed Gourcuff from Girondins Bordeaux this week, have four points from four games, the same as Lorient.
"We lacked confidence after conceding an early goal. We played better after the break, we had chances and it's a pity we could not find the back of the net," Gourcuff junior told Foot Plus TV channel.
Gourcuff looked on from the bench as Lyon conceded an early goal after a handball by centre-back Jeremy Toulalan.
Lyon lacked flair and failed to create a clear chance until Gourcuff came on for the injured Cesar Delgado on the half hour.
Kitambala made it 2-0 for the home side with a powerful left-footed shot from inside the box in the 66th minute.
Dimitri Payet scored a hat-trick as St Etienne beat Racing Lens 3-1.
Promoted Arles-Avignon are still bottom of the table without a point after losing 1-0 to Stade Rennes who moved up to second place, four points off the pace.