The 20-year-old Dane worked his way down to a 1m42.651s in the morning, edging out Red Bull's Antonio Felix da Costa by just over six hundredths of a second.
The pair finished more than three quarters of a second clear of the field, which was headed by Gary Paffett - the McLaren test driver having taken over from Magnussen for the afternoon.
Robin Frijns, this year's Formula Renault 3.5 champion, finished fourth fastest for Sauber. The 21-year-old Dutchman is set for a long-term future with the team.
Nicolas Prost (Lotus) finished fifth fastest ahead of Luiz Razia (Toro Rosso) and Giedo van der Garde (Caterham).
Razia brought about the day's only red flag 10 minutes from the finish, although he was able to return to the pits under his own power.
Magnussen will return for the final afternoon of the test with McLaren on Thursday, while da Costa - the busiest man on the opening day with 79 laps completed - will remain with Red Bull for one more day before handing the RB8 over to Frijns.
In the Dutchman's stead, Esteban Gutierrez will take over at Sauber for days two and three.
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