Gasly left it late in the session to deny Mitch Evans what would have been his first pole of the season by 0.152 seconds, with a time of 1m31.272s.
Russian Time driver Evans led the way early despite going off at Turn 1 and della Roggia a number of times but couldn't improve late.
McLaren's championship leader Stoffel Vandoorne ran consistently near the top but finished the session 0.206s off Gasly's pole time, and lines up third.
Vandoorne: I had to dominate GP2
Williams F1 development driver Alex Lynn secured fourth ahead of Rapax's Sergey Sirotkin and Campos Racing's Rio Haryanto.
Arthur Pic, Richie Stanaway, Sergio Canamasas and Alexander Rossi completed the top 10.
Racing Engineering driver Rossi attempted a different strategy to the rest of the field, following traffic issues that hampered some fast laps in qualifying at Spa.
He enjoyed a clear track for a number of laps when others came in for their mid-session tyre change and was able to jump up to eighth, before others improved.
Nissan protege Jann Mardenborough improved immensely following practice and will line up 19th on the grid, ahead of returning GP2 veteran Rene Binder.
The GP2 newcomer beat fellow rookies Patric Niederhauser and Meindert van Buuren by more than half a second, the pair to start 24th and 25th respectively.
Vandoorne seals GP2 title in Russia
Rossi wins after Lynn crashes out