Nick Cassidy set the quickest time for Envision Virgin Racing in the only practice session before qualifying in Rome.
As track conditions deteriorated due to rain, Cassidy’s 1m40.107s proved to be the time to beat.
The rain meant that the usual late flurry of 250kw laps was many seconds slower as drivers struggled for grip.
Maximillian Guenther was second for BMW with the only other representative lap at 250kw.
Behind them, Stoffel Vandoorne was third quickest for Mercedes ahead of Sergio Sette Camara in the Dragon and Oliver Rowland was fifth for Nissan.
After Saturday's dramatic opening practice session, it was a much quieter practice ahead of the second race of the weekend. There were a number of minor offs during the session, though no incident resulted in anything more than a yellow flag.
Oliver Turvey, whose car was so badly damaged in the FP1 incident he missed the race, was back on track in an entirely new NIO 333 car. Unfortunately for the Brit, he ended the session last and three seconds off the pace set by team-mate Tom Blomqvist.
Jake Dennis and Jean-Eric Vergne, who were also caught up in the same incident on Saturday, finished sixth and seventh in FP3, ahead of Sebastien Buemi, Edoardo Mortara, and Andre Lotterer.