The two McLaren juniors came out on top in a frantic scrap in the closing minutes of the session, where Antonio Felix da Costa and Marco Sorensen both briefly had spells at the top as well.
Magnussen took pole from da Costa with just two minutes remaining, and with Vandoorne running just behind him on track and taking second, the Dane managed to go even quicker next time around to give him a margin of 0.3 seconds over his main rival.
Da Costa's time was good enough to keep third, just ahead of Hungaroring race winner Nico Muller.
Sorensen appeared to have done enough to secure a top five slot, but as most of the cars headed back to the pits having used the best of their tyres already, Will Buller jumped up to fifth spot at the chequered flag.
Andre Negrao took seventh as Draco's recent improved form continued, while Nigel Melker headed Carlos Sainz and Will Stevens to complete the top 10.
Pos Driver Team Time Gap Laps 1. Kevin Magnussen DAMS 1m46.797s 12 2. Stoffel Vandoorne Fortec 1m47.097s +0.300s 13 3. Antonio F.da Costa Arden Caterham 1m47.121s +0.324s 13 4. Nico Muller Draco 1m47.173s +0.376s 12 5. William Buller Zeta Corse 1m47.255s +0.458s 13 6. Marco Sorensen Lotus 1m47.425s +0.628s 12 7. Andre Negrao Draco 1m47.476s +0.679s 13 8. Nigel Melker Tech 1 1m47.529s +0.732s 13 9. Carlos Sainz Jr. Zeta Corse 1m47.643s +0.846s 14 10. Will Stevens P1 by Strakka 1m47.690s +0.893s 13 11. Lucas Foresti Comtec 1m47.757s +0.960s 13 12. Arthur Pic AV Formula 1m47.863s +1.066s 14 13. Matias Laine P1 by Strakka Racing 1m47.918s +1.121s 13 14. Daniil Move Comtec 1m47.920s +1.123s 11 15. Norman Nato DAMS 1m47.930s +1.133s 13 16. Christopher Zanella ISR 1m48.002s +1.205s 13 17. Nikolay Martsenko Pons 1m48.055s +1.258s 11 18. Marlon Stockinger Lotus 1m48.061s +1.264s 12 19. Zoel Amberg Pons 1m48.064s +1.267s 12 20. Oliver Webb Fortec 1m48.204s +1.407s 13 21. Mikhail Aleshin Tech 1 1m48.207s +1.410s 13 22. Pietro Fantin Arden Caterham 1m48.225s +1.428s 13 23. Carlos Huertas Carlin 1m48.397s +1.600s 13 24. Jazeman Jaafar Carlin 1m48.626s +1.829s 14 25. Yann Cunha AV Formula 1m49.395s +2.598s 12
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