The first delay was required to move 2012 Moscow winner Arthur Pic's AV Formula machine from its unsafe parking position on the inside verge of Turn 12.
The top of the classification was closely balanced at the time of the stoppage. McLaren Junior driver Vandoorne was 0.051 seconds ahead of Saturday podium finisher Nigel Melker, and 0.069s clear of P1 by Strakka racer Matias Laine.
When session was restarted with a little over five minutes remaining, a flurry of improvements arrived.
Laine's team-mate Will Stevens made the most dramatic improvement. The Briton had only completed five laps prior to the red flag, but jumped from last to second position.
Stevens then sealed his highest starting position of the season when Nikolay Martsenko's sickly Pons car expired.
The Russian had reportedly deposited fluid for a few laps before coming to a smoky halt. Both Norman Nato, who spun across the grass, and Oliver Webb, who beached his car in a gravel trap, were caught by a slick surface at Turn 3.
The session was abandoned with nine seconds left to run, denying Vandoorne's rivals an opportunity to challenge his 1m20.025s pole lap.
Behind the race one victor, who enjoyed a healthy 0.415s advantage over Stevens, second to sixth was covered by just 0.1s.
Championship leader Kevin Magnussen claimed third place, ahead of Monaco winner Nico Muller and Webb.
After the disappointment of stalling while taking up his grid position on Saturday, Sergey Sirotkin bounced back to take sixth and the honour of top Russian.
Of the regular 2013 frontrunners, Red Bull junior driver Antonio Felix da Costa was the notable absence from the sharp end.
The Portuguese racer ended the morning in 13th, ahead of the session's early pole protagonist Melker, feeling the red flags ruined his best laps.
Pos Driver Team Time Gap 1. Stoffel Vandoorne Fortec 1m20.025s 2. Will Stevens P1/Strakka 1m20.440s +0.415s 3. Kevin Magnussen DAMS 1m20.472s +0.447s 4. Nico Muller Draco 1m20.475s +0.450s 5. Oliver Webb Fortec 1m20.490s +0.465s 6. Sergey Sirotkin ISR 1m20.528s +0.503s 7. Andre Negrao Draco 1m20.552s +0.527s 8. Christopher Zanella ISR 1m20.639s +0.614s 9. Mikhail Aleshin Tech 1 1m20.643s +0.618s 10. Daniil Move SMP/Comtec 1m20.661s +0.636s 11. Pietro Fantin Arden Caterham 1m20.713s +0.688s 12. Matias Laine P1/Strakka 1m20.720s +0.695s 13. Antonio Felix da Costa Arden Caterham 1m20.809s +0.784s 14. Nigel Melker Tech 1 1m20.952s +0.927s 15. Will Buller Zeta 1m21.109s +1.084s 16. Norman Nato DAMS 1m21.177s +1.152s 17. Marco Sorensen Lotus 1m21.326s +1.301s 18. Zoel Amberg Pons 1m21.487s +1.462s 19. Marlon Stockinger Lotus 1m21.496s +1.471s 20. Jazeman Jaafar Carlin 1m21.691s +1.666s 21. Nikolay Martsenko Pons 1m21.855s +1.830s 22. Mihai Marinescu Zeta 1m21.996s +1.971s 23. Arthur Pic AV 1m22.016s +1.991s 24. Carlos Huertas Carlin 1m22.139s +2.114s 25. Yann Cunha AV 1m22.381s +2.356s
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