The McLaren protege, who also took pole last time out at Spa, stood in the pits and watched his rivals fail to beat his time in the closing seconds after he had timed his second run on fresh tyres early.
The Belgian's 1m31.707s was 0.219 seconds clear of practice pacesetter Arthur Pic, who will start second for Campos Racing.
Pic was twice poised to set faster laps, but had a huge moment at Parabolica and another effort was hindered by Caterham's Rio Haryanto at Ascari much to his chagrin.
Vandoorne: I had to dominate GP2
Mitch Evans will start third for Russian Time, recovering well from an off at Lesmo 2 on his first flying lap of the session.
Series leader Jolyon Palmer qualified fourth for DAMS, this despite a late-session run-in at Parabolica with his Nemesis from Budapest, Johnny Cecotto Jr.
Raffaele Marciello was fifth fastest for Racing Engineering, ahead of Simon Trummer and Stephane Richelmi.
Title contender Felipe Nasr will start down in eighth, ahead of Carlin team-mate Julian Leal.
Series newcomer Pierre Gasly qualified 23rd for Caterham, just two places behind Cecotto.
Vandoorne seals GP2 title in Russia
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