Magnussen posted his time of 1m18.101s 90 minutes before the end of the morning's running using the C3 Pirellis, which were allocated as the softs for last weekend's Spanish Grand Prix.
Fuoco posted his fastest time on the same tyre compound during a brief spell of running between the first two of a flurry of red flags in the final hour – one caused by Daniel Ticktum's Red Bull stopping near Turn 10 and the other by the Williams of Nicholas Latifi parking near the pit exit.
Alex Albon took over the Toro Rosso from Daniil Kvyat for day two, jumping up to third place with a quick lap during the two minutes of running between the final red flag, caused by Mercedes driver Nikita Mazepin spinning at Turn 11, and the end of the session.
Alfa Romeo's Kimi Raikkonen also used C3s to set the fourth fastest time, just under half-a-second off Magnussen.
Charles Leclerc switched to Ferrari's Pirelli test car for the second day of running, ending up fifth fastest using unmarked test rubber.
That put him just ahead of Latifi, who set his best time shortly before stopping.
Mazepin had his first outing in the 2019 Mercedes, although he has been conducting a private test programme in a 2017 version.
He set the seventh fastest time on C3s, 1.045s off the pace, before his spin.
Jack Aitken was eighth fastest on his return to action for Renault, focusing on the white-banded C2 rubber, outpacing McLaren's Oliver Turvey by 0.028s.
Ticktum was 10th and did not run during the final hour of the session after the car stopped on track – the second Red Bull-triggered red flag in this test.
Lance Stroll was 11th fastest in the Pirelli test Racing Point, 0.028s faster than team-mate and simulator driver Nico Yelloly.
|3||Alexander Albon||Toro Rosso||1'18.263||+0.162s|
|4||Kimi Raikkonen||Alfa Romeo||1'18.578||+0.477s|
|10||Dan Ticktum||Red Bull||1'20.883||+2.782s|
|11||Lance Stroll||Racing Point||1'21.196||+3.095s|
|12||Nick Yelloly||Racing Point||1'21.224||+3.123s|