Antonio Felix da Costa, Carlos Sainz Jr, Nigel Malker and Stoffel Vandoorne all took brief turns at the top before DAMS driver Magnussen put in a decisive lap with two minutes remaining.
That gave him a gap of two tenths on the field at the time, and only Monaco winner Nico Muller made any inroads into that advantage to get himself on the front row for Draco in the closing stages.
Vandoorne - who had a disastrous first race at home on Saturday - abandoned his final lap and took third, and he will share the second row with race one podium finisher Melker.
Will Stevens banished the memories of an incident-filled Saturday to get into the top five, while brief provisional polesitters da Costa and Sainz were eventually shuffled back to sixth and eighth respectively.
Pos Driver Team Time Gap 1. Kevin Magnussen DAMS 1m58.428s 2. Nico Muller Draco 1m58.593s + 0.165s 3. Stoffel Vandoorne Fortec 1m58.659s + 0.231s 4. Nigel Melker Tech 1 1m58.704s + 0.276s 5. Will Stevens P1/Strakka 1m58.729s + 0.301s 6. Antonio Felix da Costa Arden Caterham 1m58.744s + 0.316s 7. Lucas Foresti Comtec 1m58.843s + 0.415s 8. Carlos Sainz Jr Zeta 1m58.972s + 0.544s 9. Carlos Huertas Carlin 1m59.102s + 0.674s 10. Mikhail Aleshin Tech 1 1m59.180s + 0.752s 11. Andre Negrao Draco 1m59.309s + 0.881s 12. Daniil Move Comtec 1m59.378s + 0.950s 13. Jazeman Jaafar Carlin 1m59.381s + 0.953s 14. Christopher Zanella ISR 1m59.387s + 0.959s 15. Matias Laine P1/Strakka 1m59.431s + 1.003s 16. Marlon Stockinger Lotus 1m59.445s + 1.017s 17. Arthur Pic AV 1m59.482s + 1.054s 18. Oliver Webb Fortec 1m59.497s + 1.069s 19. Nikolay Martsenko Pons 1m59.513s + 1.085s 20. Sergey Sirotkin ISR 1m59.547s + 1.119s 21. Marco Sorensen Lotus 1m59.724s + 1.296s 22. Pietro Fantin Arden Caterham 1m59.888s + 1.460s 23. Norman Nato DAMS 2m00.200s + 1.772s 24. Yann Cunha AV 2m00.270s + 1.842s 25. Mihai Marinescu Zeta 2m00.275s + 1.847s 26. Zoel Amberg Pons 2m00.720s + 2.292s
The 2015 Formula Renault 3.5 season will be notable for being the last with the French company's backing but also produced a worthy champion in Oliver Rowland. PETER MILLS evaluates this year's crop of drivers
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