However, Quartararo said on social media that he has been given the all-clear to ride the French MotoGP at Le Mans on 16 May.
Miller, who underwent surgery early in April, took the lead when pre-race championship leader Fabio Quartararo started to lose pace midway through the race.
MotoGP 2021: Marc Marquez escapes major injury after high-speed crash in Spanish GP practice, declared fit to continue
Marquez fell heavily in the third practice session at the circuit where last year he broke his right arm in the opening race to end his 2020 campaign.
Italian Francesco Bagnaia on a Ducati was second with Spanish world champion Joan Mir of Suzuki third.
Marquez has wasted no time getting back in the thick of things nine months after his crash in the Spanish Grand Prix which ruled him out of the entire 2020 season, and the first two races this year.
MotoGP 2021: Yamaha's Fabio Quartararo tops field following final practice, Marc Marquez in 15th position
Quartararo clocked 1min 39.044sec to finish ahead of Italians Franco Morbidelli (Petronas Yamaha SRT) and Friday pacesetter Francesco Bagnaia (Ducati Lenovo Team).
MotoGP: Returning after nine months, Marc Marquez finishes third fastest in free practice ahead of Portuguese GP
The Spaniard fared marginally less well in the second session but still produced the sixth fastest time overall to round off an exciting return, 271 days after his crash at the Spanish Grand Prix.
Marquez fractured his right arm when he fell in the first Grand Prix of last season, an injury that required three bouts of surgery, the last in December.
Spanish rookie Jorge Martin, the teammate of Zarco, was third after starting the race on pole position.
Francesco Bagnaia on another Ducati came third on his first ride in the factory team after starting on pole, beating reigning champion Joan Mir of Suzuki back into fourth in the final moments of the race
MotoGP 2021: Ducati's Francesco Bagnaia takes first pole of season in Qatar pipping Fabio Quartararo
Another Yamaha rider, Spaniard Maverick Vinales completed the front row after nudging out Italian veteran Valentino Rossi of Yamaha satellite team SRT, late in the session.
Marquez fractured his right arm on 19 July when he fell in the first Grand Prix of last season, an injury that required three bouts of surgery, the last in December.
Dovizioso, who turns 35 on 23 March, began his career in 2000 racing 125cc bikes for Aprilia. He reached MotoGP in 2008 winning 15 races and finishing runner up in the championship for three straight seasons from 2017-19 with Ducati.
"Unfortunately, all of the stands were destroyed. It also includes the press room, Race Control and the VIP rooms," Hector Farina, who owns the racetrack in the northern province of Santiago del Estero, said in a statement.
MotoGP 2021 season to begin with two races in Qatar, pre-season testing to commence in first week of March
The two night races, both to be held at the Losail circuit on 28 March and 4 April, will be followed up by the Portuguese MotoGP at the Algarve International circuit on 18 April.
Based in Bologna, Italy, Ducati entered MotoGP in 2003, securing the riders' world title with Casey Stoner in 2007.
MotoGP: Aprilia to choose between Bradley Smith, Lorenzo Savadori as replacement for banned rider Andrea Iannone
Briton Smith and Italy's Savadori filled in for Iannone this year after he was suspended for testing positive for an anabolic steroid in November 2019. His ban was recently extended from 18 months to four years.
Oliveira followed up his maiden victory in Styria in August by taking the title at Portimao in what was his first race in the premier class in his home country.
Sunday's race, held in front of empty stands due to the pandemic, provides Morbidelli with a chance to clinch second place in the world championship behind Mir.
Pole-sitter Franco Morbidelli won the race for this third victory of the season, but it was not enough to keep Mir from securing the title with one race to go