Ferrari said they were assessing new parts during the session.
The Italian team have asked for a review of the Montreal decision, with the stewards meeting Ferrari's sporting director Laurent Mekies between the two practice sessions.
Red Bull's Max Verstappen was fourth on the timesheets, 0.880 slower than Hamilton, with his car benefiting from a Honda engine upgrade.
French driver Romain Grosjean missed much of the session, completing just nine laps, after a water leak to his Haas.
Mercedes are favourites to chalk up their 10th win in a row this weekend, and eighth of the season, at a track where Hamilton won from pole last year when the French Grand Prix returned after a decade's absence.
Five-times world champion Hamilton leads Bottas by 29 points in the standings.