The McLaren Formula 1 junior, who stormed from 16th on the grid to second in race one on Saturday, took control of the session in the closing minutes, fighting off attacks from Arthur Pic and title rival Stoffel Vandoorne.
Vandoorne appeared to have secured a front row slot alongside his fellow McLaren-affiliated racer, but he was knocked back to third as last man across the line Antonio Felix da Costa pulled out a quick lap.
Da Costa's hopes of improving on the fifth place he held at the start of that lap appeared to have been ruined when a car locked up and went off ahead of him at Turn 1, but he was unaffected by that moment as he set a personal best first sector on his way to landing second place.
Vandoorne will share the second row with Marco Sorensen, while Pic had to settle for fifth after holding top spot once everyone had completed their runs on their first set of tyres.
The top six was completed by race one polesitter Andre Negrao, who had major work carried out on the electrics of his car after he was blighted by problems in Saturday's race.
Any hopes Will Stevens had of maintaining his status as a dark horse in the title race took a big hit, as he stopped very early in the session and will have to start last.
Pos Driver Team Time Gap
1. Kevin Magnussen DAMS 1m29.412s
2. Antonio Felix da Costa Arden Caterham 1m29.596s +0.184s
3. Stoffel Vandoorne Fortec 1m29.689s +0.277s
4. Marco Sorensen Lotus 1m29.777s +0.365s
5. Arthur Pic AV Formula 1m29.969s +0.557s
6. Andre Negrao Draco 1m30.158s +0.746s
7. Will Buller Zeta Corse 1m30.180s +0.768s
8. Nico Muller Draco 1m30.230s +0.818s
9. Carlos Huertas Carlin 1m30.331s +0.919s
10. Nigel Melker Tech 1 1m30.350s +0.938s
11. Oliver Webb Fortec 1m30.391s +0.979s
12. Sergey Sirotkin ISR 1m30.437s +1.025s
13. Carlos Sainz Zeta Corse 1m30.454s +1.042s
14. Marlon Stockinger Lotus 1m30.504s +1.092s
15. Christopher Zanella ISR 1m30.540s +1.128s
16. Jazeman Jaafar Carlin 1m30.614s +1.202s
17. Norman Nato DAMS 1m30.664s +1.252s
18. Mikhail Aleshin Tech 1 1m30.718s +1.306s
19. Nikolai Martsenko Pons R 1m30.783s +1.371s
20. Lucas Foresti Comtec 1m30.851s +1.439s
21. Daniil Move Comtec 1m31.016s +1.604s
22. Zoel Amberg Pons 1m31.020s +1.608s
23. Matias Laine P1 1m31.048s +1.636s
24. Pietro Fantin Arden Caterham 1m31.210s +1.798s
25. Yann Cunha AV Formula 1m31.649s +2.237s
26. Will Stevens P1 no time
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