The 19-year-old Italian, leading the world championship after four successive victories, went 0.043 quicker than Red Bull's Verstappen, who will start on the front row.
Ferrari, strongly tipped as race favourites, had to be content with the second row on Sunday's grid with Lewis Hamilton third quickest, 0.228 slower, and local favourite Charles Leclerc, winner of the race in 2024, fourth.
Isack Hadjar, in the second Red Bull, was fifth, with Antonelli's teammate George Russell a disappointing sixth.
Reigning world champion and last year's Monaco winner Lando Norris will be on the fourth row alongside fellow McLaren driver Oscar Piastri.