The Dane, who was in action earlier this week for McLaren at Formula 1's young driver test, led the way for much of the afternoon session and then responded in the closing stages as the majority of the field started to improve.
Magnussen briefly lost top spot to fellow Dane Marco Sorensen, but seconds after the Lotus driver went even quicker to extend his gap at the front, Magnussen went faster still.
A red flag with just over a minute to go halted several other drivers who were on course to improve, including Nigel Melker who had just gone fastest through the first sector.
Magnussen's effort was half a second quicker than the pace had been in the morning session - when likely Sauber 2014 F1 racer Sergey Sirotkin had led a one-two for ISR.
The Czech team was competitive again in the afternoon with Christopher Zanella best of the rest in third, but he was four tenths of a second adrift of the Danish pair out front.
Melker finished the session fourth, ahead of Sirotkin, while Arthur Pic was another driver to improve late on to push Red Bull junior Antonio Felix da Costa down to seventh.
Da Costa was one of several drivers to have lap times deleted earlier in the session for exceeding track limits.
Other frontrunners affected were Magnussen and Sirotkin, and over the course of the 60-minute session race control sent nearly 30 messages to teams warning them about the track limits.
Practice one:Pos Driver Team Time Gap 1. Sergey Sirotkin ISR 1m17.572s 2. Christopher Zanella ISR 1m17.646s +0.074s 3. Arthur Pic AV 1m17.836s +0.264s 4. Marco Sorensen Lotus 1m18.015s +0.443s 5. Nico Muller Draco 1m18.070s +0.498s 6. Marlon Stockinger Lotus 1m18.081s +0.509s 7. Yann Cunha AV 1m18.105s +0.533s 8. Nikolay Martsenko Pons 1m18.109s +0.537s 9. Norman Nato DAMS 1m18.119s +0.547s 10. Stoffel Vandoorne Fortec 1m18.217s +0.645s 11. Riccardo Agostini Zeta Corse 1m18.338s +0.766s 12. Pietro Fantin Arden Caterham 1m18.372s +0.800s 13. Nigel Melker Tech 1 1m18.482s +0.910s 14. Kevin Magnussen DAMS 1m18.487s +0.915s 15. Matias Laine P1/Strakka 1m18.490s +0.918s 16. Carlos Huertas Carlin 1m18.544s +0.972s 17. Jazeman Jaafar Carlin 1m18.623s +1.051s 18. Will Stevens P1/Strakka 1m18.631s +1.059s 19. Zoel Amberg Pons 1m18.648s +1.076s 20. Oliver Webb Fortec 1m18.703s +1.131s 21. Andre Negrao Draco 1m18.867s +1.295s 22. Will Buller Zeta Corse 1m18.871s +1.299s 23. Antonio Felix da Costa Arden Caterham 1m19.108s +1.536s 24. Lucas Foresti Comtec 1m19.521s +1.949s 25. Daniil Move Comtec 1m19.656s +2.084s 26. Mikhail Aleshin Tech 1 1m19.785s +2.213s Practice two:Pos Driver Team Time Gap 1. Kevin Magnussen DAMS 1m17.055s 2. Marco Sorensen Lotus 1m17.151s +0.096s 3. Christopher Zanella ISR 1m17.501s +0.446s 4. Nigel Melker Tech 1 1m17.536s +0.481s 5. Sergey Sirotkin ISR 1m17.548s +0.493s 6. Arthur Pic AV 1m17.588s +0.533s 7. Antonio Felix da Costa Arden Caterham 1m17.589s +0.534s 8. Marlon Stockinger Lotus 1m17.632s +0.577s 9. Oliver Webb Fortec 1m17.649s +0.594s 10. Stoffel Vandoorne Fortec 1m17.681s +0.626s 11. Carlos Huertas Carlin 1m17.818s +0.763s 12. Nikolay Martsenko Pons 1m17.959s +0.904s 13. Will Buller Zeta Corse 1m17.988s +0.933s 14. Andre Negrao Draco 1m18.035s +0.980s 15. Norman Nato DAMS 1m18.074s +1.019s 16. Will Stevens P1/Strakka 1m18.098s +1.043s 17. Yann Cunha AV 1m18.219s +1.164s 18. Nico Muller Draco 1m18.235s +1.180s 19. Lucas Foresti Comtec 1m18.317s +1.262s 20. Jazeman Jaafar Carlin 1m18.330s +1.275s 21. Zoel Amberg Pons 1m18.416s +1.361s 22. Daniil Move Comtec 1m18.481s +1.426s 23. Riccardo Agostini Zeta Corse 1m18.657s +1.602s 24. Matias Laine P1/Strakka 1m18.905s +1.850s 25. Pietro Fantin Arden Caterham 1m19.011s +1.956s 26. Mikhail Aleshin Tech 1 1m19.510s +2.455s
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