A 30-minute delay halted proceedings while an oil spill from an earlier session was cleared from Turn 13, though the circuit remained soaked despite the rainfall stopping during the delay.
Once underway, Kawasaki’s Leon Haslam set the early pace at 2m00.283s, though was immediately beaten by Friday practice pacesetter van der Mark on the Crescent-run Yamaha, who fired in a 1m59.356s.
Honda’s Leon Camier briefly held top spot, but reigning world champion Rea moved the goalposts substantially with a 1m56.424s after five minutes of running.
The KRT rider found another eight tenths on his follow-up tour, which put him a second clear of the Ten Kate Yamaha of home hero Loris Baz.
Van der Mark reduced Rea’s advantage to six tenths soon after, though the Kawasaki rider once again upped his pace to produce a 1m53.956s to move over a second out of reach again.
The Yamaha rider proceeded to scythe his deficit to Rea over a series of laps in the closings stages, and put on a challenge for pole on his final tour.
However, van der Mark could not usurp Rea from top spot, missing out by 0.013s with a 1m53.969s.
At the same time, Rea was setting the timing screens alight, but came up on yellow flags for a crash for Sylvain Barrier (Brixx Ducati) and traffic in the last sector.
He still found 0.001s to improve to a 1m53.955s to cements his sixth pole of the season, while Haslam completes the front row in third on the sister works ZX-10RR.
Barni Ducati’s Michael Ruben Rinaldi leaped up to fourth at the end with a 1m54.563s, beating Baz and BMW’s Tom Sykes to head row two.
Alex Lowes will start today’s first feature race and Sunday’s sprint race from seventh on the sister works Yamaha, with Eugene Laverty (Go Eleven Ducati) and the Honda duo of Ryuichi Kiyonari and Camier rounding out the top 10.
Bautista, who trails Rea by 91 points ahead of this afternoon’s race, opted to sit out Friday’s soaked second practice having only completed a handful of laps in FP1 on his first visit to Magny-Cours.
In the 25-minute Superpole session, the Ducati rider failed to find much form and ended up 2.5s off the pace in 14th, while Puccetti’s Toprak Razgatlioglu was a further six tenths slower in 16th.
Bautista’s teammate Chaz Davies crashed late on at the Imola chicane, leaving him 11th. GRT Yamaha’s Marco Melandri also fell at Turn 13, consigning him to 13th.