The Italian Ducati rider topped the timesheets with a fastest lap of one minute and 37.866secs at the circuit in central France, with Ireland's Eugene Laverty (Voltcom Crescent) 0.272secs behind in second.
Home favourite Sylvain Guintoli (1:38.152) was third for Aprilia as he displayed better pace than defending champion Tom Sykes of Great Britain (1:38.518), the Kawasaki rider only good enough for sixth behind Pata Honda's Jonathan Rea (1:38.157) and team-mate Marco Melandri (1:38.451).
Earlier, Frenchman Guintoli went fastest in the first free practice with a time of one minute and 38.366secs, beating Sykes - winner of both races at Magny-Cours in 2013 - by 0.286secs.
Guintoli's apparent extra speed should give him added confidence going into Saturday's qualifying session and the two races on Sunday as he bids to cut into Sykes' healthy lead at the top of the standings and keep his championship hopes alive ahead of the final race weekend in at Losail next month.
Sykes leads Guintoli by 31 points having claimed eight victories and finished on the podium in all but six races in the 2014 season.