The Dutchman's run of nine successive wins was also snapped as he broke down on lap four with a brake problem, two years after his and Red Bull's last retirement due to a mechanical issue at the 2022 Albert Park race.
Red Bull's reliability has underpinned Verstappen's run to the last three drivers' championships and the team's two successive constructors' titles.
So the setback for pole-sitter Verstappen was a sobering moment for the Milton Keynes-based team, who are now just four points clear of Ferrari in both title races following Carlos Sainz's triumph in Australia.
"We are all one team and that DNF hurts everybody in the same way," Red Bull boss Christian Horner told reporters.
"It's a matter of learning from it. We've had two years of no mechanical DNFs which has been remarkable.
"(It's) remarkable after three races that he's still leading the championship even with that DNF," added Horner of Verstappen.
The driver said his car had felt fine during the formation lap but the right rear brake was stuck from the start of the race.
"Of course, the temperature kept on increasing," Verstappen told reporters.
"So it was also basically driving with the handbrake on and that's why already it felt the car was really weird to drive in some corners."
Sergio Perez, runner-up behind Verstappen at both Bahrain and Saudi Arabia, was fifth for Red Bull on Sunday and complained his car was lacking pace and proved troublesome throughout the weekend.
Horner said Perez was probably not aware he had picked up some damage when passing Aston Martin's Fernando Alonso during the race.
"He lost a significant amount of downforce from the floor of the car," added Horner.
"Then as soon as you get that your tyre degradation gets worse and we were just not good at the end of the stints, which is a bit of an unusual trait for our car."
Ferrari celebrated maximum points, with runner-up Leclerc also clocking the fastest lap.
Perez said Ferrari "absolutely" had the pace to win, even if Verstappen had stayed on track to the finish.
"It's a very bad weekend. We never managed to get in the window (of performance) with the car and look after the tyres," added the Mexican driver.
