Carlin driver Palmer lapped the Italian GP venue in 1:32.120s, just three thousandths of a second faster than Racing Engineering's Fabio Leimer. Palmer was fastest in the first and third sectors, with Leimer gaining his time in the second.
Leimer's fellow title contender Sam Bird was third quickest for Russian Time. Stephane Richelmi was a late improver, up to fourth for DAMS, as team-mate Marcus Ericsson was only ninth and forced to pull off at Rettifilo near the end of the session.
Bird's team-mate Tom Dillmann was fifth fastest, ahead of points leader Stefano Coletti, whose session was ruined when he ran into the back of Johnny Cecotto Jr at the exit of Rettifilo, breaking his front wing, an incident that has been referred to the stewards.
The session was previously interrupted after five minutes when Cecotto ran into the gravel at Parabolica and he spun across the track as he tried to rejoin, stranding him sideways in the middle of track and causing a red flag.
Of the other title contenders, Felipe Nasr was only 15th, but aborted a couple of quicker laps. James Calado, fresh from FP1 running with Force India, set the early pace but ended the session 11th.
Other incidents included Sergio Canamasas spinning off at Ascari, Rene Binder's engine cover coming off, and Jon Lancaster, returning in place of Robin Frijns at Hilmer, going off briefly at Lesmo 2.
Series debutant Sergio Campana, who replaces Ricardo Teixeira at Trident, was slowest, 2.3s off the pace.