The 19-year-old qualified 0.222 seconds faster than championship-leading teammate George Russell, who secured the Mercedes front row lockout after earlier car trouble.
Ferrari's Lewis Hamilton was third fastest, a strong position for the seven-time world champion who can hope for a quick start on Sunday.
Antonelli was already the youngest pole sitter in any format after leading qualifying for last year's Miami sprint, but in Shanghai on Saturday, he demolished Sebastian Vettel's previous Grand Prix record that the German set as a 21-year-old in 2008.
"It was a pretty clean session, so I'm really happy," said Antonelli.
"I saw he (Russell) had the issue and tried to keep my focus to stay calm and deliver a good lap."
No battery and stuck in gear
Russell got in only one lap after coming to a halt on track early in the final phase and complaining over the radio that there was no battery and he could not shift gear.
The Briton managed to get the car going again and returned to the pits, where mechanics worked flat out to get him back out before the chequered flag.
"Definitely damage limitation," said Russell, who won the earlier sprint to go 11 points clear at the top but was staring at 10th on the grid until the dying seconds.
"Q2, the front wing broke, we were wrapping our heads around that. Then obviously went out in Q3, car stopped on track, car wasn't restarting, couldn't change gear.
"Starting the last lap I had no battery, no tyre temp, no nothing. But the team have done a really great job to get us into this position, it could have been much worse."
Ferrari's Charles Leclerc qualified fourth with the McLarens of Oscar Piastri and reigning champion Lando Norris fifth and sixth.
"It is still going to be a challenge, but I'm sure we'll have some fun," said Hamilton, who was third in the sprint with Leclerc second.
"I'm looking forward to it. We learnt a lot in the sprint race. Our goal is to break the gap between these guys (Mercedes) somehow."
Leclerc said he had been struggling at the track and had done his best.
"These cars have to be driven a bit differently in qualifying so there is some work going on to try and optimise everything which will put us closer to Mercedes eventually," added the Monegasque.
Verstappen not enjoying his Red Bull
Pierre Gasly qualified seventh for Renault-owned Alpine, with four-time world champion Max Verstappen eighth for Red Bull and the Dutch driver's new teammate Isack Hadjar ninth.
"It's incredibly tough to drive," Verstappen said of his car. "There's no balance, I cannot lean on the car, every lap is a fight.
"Every time I did another lap on a tyre set it felt awful. I honestly think it's going to be quite tough tomorrow.
"In the past sometimes we would turn it upside down and it would work. Now nothing works. It's just not nice. I cannot push ... I am not enjoying it at all."
Oliver Bearman completed the top 10 for Ferrari-powered Haas, continuing a strong start to the season by the young Briton.
Williams, Aston Martin and newcomers Cadillac were the teams whose drivers failed to progress from the opening phase.
Cadillac's experienced Finn Valtteri Bottas outqualified Aston's Lance Stroll while Williams continued to struggle with an overweight car.
"Terrible!" Williams driver Alex Albon shouted in frustration over the car radio after qualifying in 18th position.
