The teenage Mercedes driver blazed to a best time of one minute and 44.361 seconds, 0.317 seconds ahead of Red Bull's Max Verstappen, while Lando Norris was third fastest in his McLaren but will start with a 10-place grid penalty.
As he crossed the line after crushing his rivals with a ferocious last lap, the pit reminded Antonelli that it was his father's birthday.
"Happy birthday, Dad!" he responded.
In his on-track interview, the Italian said he was happy with his display.
"It was not a very straightforward session. The track changed a lot," said Antonelli.
"The last lap was good. It was a nice lap. It was very clean, so very happy.
"Tomorrow is another day, with Max starting next to me it will be important to get a good start and be ahead into Turn 5."
In a session briefly red-flagged because of gravel on the track, Antonelli's team-mate George Russell was fourth fastest and will share the second row with Charles Leclerc of Ferrari.
The second Ferrari of Lewis Hamilton was next, followed by Oscar Piastri in a McLaren.
Verstappen was able to grab Isack Hadjar's slipstream for his final lap.
"It was definitely helping me, otherwise I would not be standing here, I would be P6 or something," the Dutchman said.
"Isack did a really good job. Tomorrow I will be looking in my mirrors, but today was a decent result."
Like Norris, Hadjar, Fernando Alonso and Lance Stroll all start tomorrow with grid penalties for power unit changes.