The Dane, who sealed the title with a win in race one, withstood pressure from fellow McLaren junior and championship runner-up Stoffel Vandoorne in the first stint of the race, after the latter had pulled a spectacular pass on Arthur Pic at Turn 1 to re-take second.
But Magnussen was biding his time, and after the mandatory pitstops he unleashed his pace to build up a dominant lead.
Once that gap was up to nearly 12 seconds the champion backed off, while Vandoorne had to focus on keeping race one runner-up Will Stevens behind for second.
Stevens had jumped from fifth to third during the stops, but after hassling Vandoorne for a few laps he eventually settled into a safe podium finish.
Pic, who had been a factor in the lead fight after a fast start, lost time during his pitstop and then retired two corners later with an apparent loose right rear wheel.
That left Nico Muller, who had also been on the tail of the lead fight before Magnussen's pace strung the field out, to take fourth ahead of a closely contested fight for fifth.
That battle was headed by Magnussen's DAMS team-mate Norman Nato, as he managed to keep Carlos Sainz Jr and Marco Sorensen at bay.
Sorensen was one of the big movers in the field, using the strategy of making a late pitstop to allow him to run in clean air as he climbed from a lowly starting position of 16th.
Results - 29 laps: Pos Driver Car Time/Gap 1. Kevin Magnussen DAMS 45m52.547s 2. Stoffel Vandoorne Fortec +8.962s 3. Will Stevens P1/Strakka +12.097s 4. Nico Muller Draco +20.437s 5. Norman Nato DAMS +22.274s 6. Carlos Sainz Jr Zeta +23.171s 7. Marco Sorensen Lotus +23.515s 8. Nigel Melker Tech 1 +31.579s 9. Marlon Stockinger Lotus +32.027s 10. Oliver Webb Fortec +32.649s 11. Christopher Zanella ISR +35.790s 12. Zoel Amberg Pons +36.323s 13. Antonio Felix da Costa Arden Caterham +36.931s 14. Mikhail Aleshin Tech 1 +50.512s 15. Lucas Foresti SMP/Comtec +51.006s 16. Matias Laine P1/Strakka +52.293s 17. Nikolay Martsenko Pons +52.785s 18. Carlos Huertas Carlin +1m01.264s 19. Yann Cunha AV +1m32.855s 20. Pietro Fantin Arden Caterham -1 lap Retirements: William Buller Zeta 20 laps Andre Negrao Draco 17 laps Arthur Pic AV 12 laps Daniil Move SMP/Comtec 12 laps Sergey Sirotkin ISR 3 laps
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