The 19-year-old set the fastest time of 01:28.778 seconds on his first attempt in the final shootout phase of qualifying.
A lock-up on his second attempt prevented him from going even faster, but it did not matter, with his initial effort good enough to beat second-placed Mercedes teammate George Russell by a handy 0.298 seconds.
"Putting that one lap in that was very good - Bono (Antonelli's engineer Peter Bonnington) told him to put a banker in," Mercedes team chief Toto Wolff told Sky Sports.
"And then he pushed it a little bit hard on the last one, and it wasn't so good, but it's really pleasing to see," he added.
Drivers typically put in two fast laps when battling for pole.
The first is usually treated as a "banker" attempt, aimed at getting a lap time on the board during which drivers tend to play it slightly safe before putting it all on the line in a high-risk last-gasp blast for top spot.
For Antonelli, playing it safe paid off.
He heads into the weekend fired up from having secured his first pole and victory two weeks ago in China as he bids for a first win at Suzuka, an old-school layout renowned as one of the great drivers' tracks.
"When you hear his radio communications, also on the intercom in the garage, it's just calm," Wolff added.
"Not putting himself too much under pressure."