The Spaniards claimed a win apiece at the last two rounds in Austin and Jerez, and the Repsol factory bikes were once again the class of the field on the tight and twisting Bugatti configuration of the Le Mans circuit.
Pedrosa topped both the morning and afternoon running, with his lap of one minute 34.035 seconds during the second session being the quickest of the day, allowing him to edge out rookie Marquez by less than two-tenths of a second.
Valentino Rossi was the quickest of the factory Yamahas as he got the better of team-mate and world champion Jorge Lorenzo to claim the third-fastest time.
Stefan Bradl produced his best Friday performance of the season to date to take fifth on his LCR Honda, with Britain's Cal Crutchlow sixth aboard his Tech 3 Yamaha at the end of a week where his future in the team has been thrown into doubt.
Andrea Dovizioso and Nicky Hayden were next up on the factory Ducatis, with Alvaro Bautista and Aleix Espargaro, on the fastest of the CRT machines, rounding out the top 10.
Bradley Smith was 11th on the second Tech 3 bike, while Pramac Ducati's Andrea Iannone was 12th after a difficult session which included a heavy fall at the last corner.