The wet, cold conditions led to a multitude of fallers including championship leader Sandro Cortese (Ajo KTM) and Monlau Honda's Miguel Oliveira, who was on provisional pole when he lost the bike at the Turn 10 chicane halfway into the session.
Maverick Vinales (Avintia FTR-Honda) had been battling with Oliveira until the latter's fall, but moved into a class of his own as the session progressed and conditions gradually improved.
The 17-year-old Spaniard lowered his own personal best mercilessly, dipping down into the 1m55s to eventually finish the session almost one second clear of the field.
Despite being unable to get going following his crash - and therefore missing out on the optimum conditions - Oliveira remained second right up until the chequered flag, when Laglisse Honda's Efren Vazquez did enough to demote him to the final spot on the front row.
Jakub Kornfeil (Ongetta FTR-Honda) deprived Alexis Masbou (Caretta Honda) a fourth-place start for his home grand prix.
After his early fall, Cortese meanwhile pushed his bike back to the pits and was able to rejoin the action in the final minutes. He got himself up into sixth, finishing as the highest non-Honda rider.
Kalex KTMs locked out the third row, with Alberto Moncayo, Hector Faubel (both Aspar) and Luis Salom (RW) in seventh, eighth and ninth respectively.
The tough conditions impacted hard on the Mahindra team, with both Danny Webb and Marcel Schrotter falling and qualifying outside the 107 per cent mark. Ioda Team Italia's Luigi Morciano was also outside the mark.