Marcelo Bielsa's men had looked an unstoppable force at the summit of the French top flight, having scored a total of 22 goals on their winning streak.
However, in Lyon they came up against a side who themselves were defending a six-game unbeaten run and the home side looked reluctant to give up that record without a fight.
Anthony Lopes did brilliantly to keep out an Andre Ayew volley at the other end, but Gourcuff's persistence eventually paid off as he scored the only goal of the match - a rifled effort from 12 yards - in the 65th minute.
Lyon could have put the result beyond all doubt in stoppage time, but Mandanda did well to keep out substitute Clinton N'Jie.
The hosts climb to third in the Ligue 1, while Marseille's cushion over champions Paris Saint-Germain at the top now stands at four points.
Ligue 1's basement club had won at Lille last time out to call time on a four-match losing streak, and that momentum looked set to continue when Claudio Beauvue opened the scoring in the eighth minute.
Guingamp's reprieve did not last long, however, as Eric Bautheac found the net a minute later to round off a sensational day at the office for Nice, who climb to seventh.
Saint-Etienne went fourth courtesy of a 1-0 victory over Metz - Max Gradel scoring the only goal of the encounter.
In the day's other match, Rennes subjected Lille to a third successive defeat with a 2-0 win at Stade de la Route de Lorient.
