The McLaren junior, who only needs to finish sixth to be assured of the title before Sunday's season finale, controlled the session from start to finish.
Magnussen and DAMS team-mate Norman Nato led the way after the first runs of the session, but while Nato would slip back as the times improved, Magnussen was able to respond to everything his rivals could throw at him to take his seventh pole position of the season.
After the Dane had kicked off the final flurry of activity by beating his own best lap with five minutes to go, that effort was beaten by Carlos Sainz Jr, Nigel Melker, Will Buller and Will Stevens.
But Magnussen was patient, backing off before launching another bid for pole and beating Stevens by a tenth of a second.
His title rival Stoffel Vandoorne tried a similar tactic, but after going second to Magnussen on his first attempt he could only recover to fourth with his final hot lap. Britons Stevens and Buller split the title rivals on the grid, while behind Vandoorne the top six was completed by Marco Sorensen and Sergey Sirotkin.
Melker, Sainz and Nato were shuffled back to seventh, eighth and ninth respectively after their brief heroics earlier on, while Red Bull junior Antonio Felix da Costa - who won both races at Barcelona last year - could only manage 10th on the grid.
Only 25 cars will take part in the race, as Jazeman Jaafar is not fit to compete having been taken to hospital with an infection, which also forced him to miss free practice on Friday.
Pos Driver Team/Car Time Gap
1. Kevin Magnussen DAMS 1m29.618s
2. Will Stevens P1/Strakka 1m29.725s +0.107s
3. William Buller Zeta 1m29.885s +0.267s
4. Stoffel Vandoorne Fortec 1m29.932s +0.314s
5. Marco Sorensen Lotus 1m29.961s +0.343s
6. Sergey Sirotkin ISR 1m29.981s +0.363s
7. Nigel Melker Tech 1 1m30.020s +0.402s
8. Carlos Sainz Jr Zeta 1m30.034s +0.416s
9. Norman Nato DAMS 1m30.078s +0.460s
10. Antonio Felix da Costa Arden Caterham 1m30.208s +0.590s
11. Nico Muller Draco 1m30.306s +0.688s
12. Mikhail Aleshin Tech 1 1m30.333s +0.715s
13. Marlon Stockinger Lotus 1m30.358s +0.740s
14. Arthur Pic AV 1m30.381s +0.763s
15. Matias Laine P1/Strakka 1m30.599s +0.981s
16. Christopher Zanella ISR 1m30.601s +0.983s
17. Andre Negrao Draco 1m30.662s +1.044s
18. Oliver Webb Fortec 1m30.675s +1.057s
19. Nikolay Martsenko Pons 1m30.783s +1.165s
20. Zoel Amberg Pons 1m30.799s +1.181s
21. Daniil Move SMP/Comtec 1m30.812s +1.194s
22. Lucas Foresti SMP/Comtec 1m30.868s +1.250s
23. Pietro Fantin Arden Caterham 1m30.907s +1.289s
24. Yann Cunha AV 1m31.126s +1.508s
25. Carlos Huertas Carlin 1m31.185s +1.567s
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