The 19-year-old Italian, chasing a fourth win in a row, lapped the Circuit Gilles Villeneuve with a best time of one minute 13.402 seconds in bright sunshine and cool conditions.
Team mate George Russell, last year's winner in Montreal and seeking to regain momentum after Antonelli's sizzling start to the season, was second fastest and 0.142 slower.
The Briton ended his session with a spin at Turn Two and glanced against the barrier, bringing out yellow flags.
Ferrari's seven-times world champion Lewis Hamilton was third fastest, ahead of team mate Charles Leclerc, with Red Bull's four-times champion Max Verstappen fifth.
McLaren's reigning champion Lando Norris was sixth fastest, with team mate Oscar Piastri seventh.
The 60-minute session, the only practice before sprint qualifying later on Friday, was interrupted by three red flags and then extended to make up for lost track time.
Racing Bulls' Liam Lawson stopped on track after losing power steering nine minutes into the session, causing the first stoppage.
Williams' Alex Albon then crashed at Turn Seven after he was unable to avoid a groundhog, bringing out the second red flag.
A final stoppage came five minutes from the end after Esteban Ocon stopped on track.
Racing Bulls' Arvid Lindblad was a surprise eighth fastest, with Audi's Nico Hulkenberg ninth and Aston Martin's Fernando Alonso completing the top 10.
Mercedes brought heavily revised aerodynamic components to Montreal, targeting improved downforce and flow structure, after rivals McLaren, Ferrari and Red Bull introduced upgrades at Miami earlier this month.
Qualifying for the points-paying Saturday sprint follows later on Friday.