The McLaren junior, who topped all three tests prior to qualifying at the Spanish track, was involved in the fight for pole from the start of the wet session.
Initially he was scrapping with championship leader Stoffel Vandoorne at the top, but the Belgian was unable to stay in the pole fight as the track started to dry and times improved in the closing stages.
Magnussen's countryman Marco Sorensen took up the fight along with Red Bull junior Antonio Felix da Costa, but every improvement they made was bettered by the DAMS driver.
The polesitter's session was not without drama though. On one lap he managed to go quickest despite a clash with Nico Muller at the final hairpin.
He had a couple of off-track moments as he pushed the limits more than most, and his final lap - which was already slightly slower than his best - was ruined by traffic.
Da Costa was on course to snatch pole with his final lap as the chequered flag came out, but the Portuguese driver's effort faded and he had to make do with third.
There was then concern at Arden Caterham when da Costa then stopped on track before getting back to the pits.
"I don't know what caused it yet," da Costa said. "I just saw some alarms on the dash. Now we have to wait to find out."
For the second event running the ISR cars proved to be a wildcard in the pole fight. Sergey Sirotkin briefly took pole from Magnussen with two minutes to go, while team-mate Christopher Zanella held third before da Costa's final lap.
The Czech team will line up second and fourth respectively, just ahead of Sorensen and Arthur Pic.
Vandoorne, who showed frontrunning pace in the wet in practice, slipped back to ninth, which he put down to starting his second run too early.
"I did my quickest time when the track was still a bit too wet," he told AUTOSPORT. "By the end when it was quicker my tyres were burned.
"It'll be a hard race, but at least we know we are not back there because we don't have the pace."
Pos Driver Team Time Gap Laps
1. Kevin Magnussen DAMS 1m54.306s 13
2. Sergey Sirotkin ISR 1m54.342s + 0.036s 12
3. Antonio F. da Costa Arden Caterham 1m54.526s + 0.220s 15
4. Christopher Zanella ISR 1m54.547s + 0.241s 11
5. Marco Sorensen Lotus 1m54.675s + 0.369s 15
6. Arthur Pic AV Formula 1m55.007s + 0.701s 13
7. Norman Nato DAMS 1m55.072s + 0.766s 13
8. Nico Muller Draco 1m55.086s + 0.780s 13
9. Stoffel Vandoorne Fortec 1m55.157s + 0.851s 15
10. Oliver Webb Fortec 1m55.312s + 1.006s 15
11. Daniil Move Comtec 1m55.475s + 1.169s 12
12. Nigel Melker Tech 1 1m55.546s + 1.240s 12
13. Will Stevens P1 1m55.619s + 1.313s 14
14. Andre Negrao Draco 1m55.669s + 1.363s 13
15. Matias Laine P1 1m55.709s + 1.403s 13
16. Mikhail Aleshin Tech 1 1m55.716s + 1.410s 13
17. N.Martsenko Pons 1m55.721s + 1.415s 13
18. M.Stockinger Lotus 1m55.752s + 1.446s 14
19. Lucas Foresti Comtec 1m55.944s + 1.638s 13
20. Pietro Fantin Arden Caterham 1m56.004s + 1.698s 15
21. Zoel Amberg Pons 1m56.228s + 1.922s 14
22. Jazeman Jaafar Carlin 1m56.404s + 2.098s 14
23. Matheo Tuscher Zeta Corse 1m56.647s + 2.341s 13
24. Yann Cunha AV Formula 1m56.677s + 2.371s 14
25. Mihai Marinescu Zeta Corse 1m57.372s + 3.066s 13
26. Carlos Huertas Carlin 1m57.778s + 3.472s 14
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