The Frenchman responded to a difficult Friday to set a fastest time of 1m58.226s, edging out Aragon winner Aurelien Panis by 0.143 seconds.
"We had brake and gearbox problems on Friday, and we decided to change the gearbox overnight," explained Vaxiviere, who has had a relatively slow start to 2016 after finishing runner-up in last year's title race.
"I treated my first run in qualifying a little bit like an FP3, trying to understand if we had made the right choice with the gears. Then at the end we put everything together.
"I am really happy with the lap and to give SMP Racing its first 3.5 pole - I think we're back now."
Qualifying was interrupted by a red flag period in the middle of the session when gentleman racer Giuseppe Cipriani stranded his Durango machine at the Bus Stop chicane.
"The red flag actually helped us out by giving us more time to prepare for my final run," added Vaxiviere.
"I think everyone appreciated this red flag."
Panis's front row start marked a return to form following a difficult Friday when he finished in the penultimate position in both practice sessions.
"The team worked really hard last night," said Panis.
"We tried low and medium-downforce set-ups, and weren't really going for outright performance, although we knew we needed to make some improvements to the car.
"For qualifying we opted for medium rather than low-downforce, but we're still deciding what to do for the race."
Panis's Arden team-mate Egor Orudzhev held provisional pole until two minutes before the chequered flag in the half-hour session, when he was demoted by Vaxiviere.
Orudzhev would finish third, ahead of Friday's form man Rene Binder and AVF's championship leader Tom Dillmann.
Formula Renault 2.0 NEC champion Louis Deletraz completed the top six for Fortec, from Yu Kanamaru and Binder's Lotus team-mate Roy Nissany.
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