Miller, who won the last race in Spain, finished ahead of French pair Johann Zarco, riding for Ducati's satellite Pramac team, and Fabio Quartararo, on a Yamaha.
With intermittent rain making life difficult at the Bugatti circuit Quartararo topped the timesheets from his Yamaha teammate Maverick Vinales with Ducati's Jack Miller completing the front row.
The race was scheduled to take place on 11 July at the new KymiRing circuit which should have hosted its first MotoGP race last year.
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.
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.
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.
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.
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.