Six-time elite class champion Márquez was set fair to make it six wins out of six in Texas after romping to victories in the sprints and main races in Thailand, Argentina and Saturday’s sprint in Austin.
But a crash on lap nine did it for the Spanish superstar, gifting victory to his Ducati factory teammate.
Alex Márquez, on a Ducati satellite bike, took second for the sixth time to move one point clear of his older brother in the riders’ standings.
Fabio Di Giannantonio, on another Ducati satellite machine, came in third at the Circuit of the Americas.
Bagnaia supplied Ducati with their 20th consecutive grand prix success, just two shy of Honda’s historic benchmark of 22.
There was chaos before lights out with riders on the grid, their bikes equipped with wet tyres, all set for the start.
But then, with the changeable overcast conditions drying, pole-sitter Marc Márquez dramatically ran back to the pits to swop to a bike with slicks, triggering a domino effect as his grid rivals copied his example.
As he had not sat on his bike Márquez did not break any rules, only causing mayhem, and a delayed start with a race reduced by one lap to 19 laps.
There was one last twist to the pre-race drama, when Maverick Vinales, last year’s winner, had to wheel his bike off the grid with an issue to start from the pits.
Márquez got away to a flyer when they were eventually let go to lead from Alex Márquez with Bagnaia up from sixth to third.
Márquez senior quickly stamped his authority on the race with more than a one second cushion over the chasing pack.
Bagnaia moved up to second after eight laps, albeit over two seconds behind the rider who lists the Circuit of the Americas (COTA) as one of his favourite tracks.
Then the race was turned on its head when Márquez crashed on lap nine, slithering off his bike after touching a kerb.
He rejoined in 18th place with 10 laps remaining, only to call it a day a couple of laps later.
One frustrated bystander at COTA was world champion Jorge Martin who has missed the opening three rounds after breaking his right hand and foot in pre-season testing crash in Malaysia.
That has delayed his title defence and his debut for Aprilia. He moved to the team after being overlooked by Ducati for the factory ride that was offered to Márquez.
The Spaniard faces a seemingly Herculean task though to defend his title when he resumes in Qatar next time out, lagging 87 points behind Alex Márquez on his belated seasonal bow, with Marc Márquez on 86, and Bagnaia third on 75 points. (AFP)
