The 2013 double victor opted to avoid any traffic issues by circulating on his own while rival competitors took their mid-session change of tyres.
Vandoorne was rewarded by moving to the head of the classification with a time of 1m21.208s, but the action would intensify, and lap times lower, in the session's final 15 minutes.
Friday afternoon pacesetter Antonio Felix da Costa found a tenth of a second to demote Vandoorne from provisional pole with six minutes left on the clocks, before debutant Will Buller caused the major upset of the weekend.
The European Formula 3 graduate, acclimatising to his first meeting with 2013 newcomer Zeta Corse, achieved an astounding breakthrough in performance to jump from 15th to first.
Vandoorne swiftly reasserted his authority by moving back to the head of the pack.
The reigning Formula Renault 2.0 Eurocup champion subsequently improved on his time to record the eventual pole lap of 1m20.283s, and briefly enjoy a half-second margin over second-placed Nigel Melker.
Da Costa found significant gains on his last lap to move within 0.036s of Vandoorne, and will join his title rival on the front row for Saturday afternoon's race.
Championship leader Kevin Magnussen survived an early off-track excursion at Turn 3 to squeeze into third, 0.001s ahead of one of the stars of Spa-Francorchamps' second race in Melker.
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