Over the remaining thirteen laps, he opened up a healthy advantage at the front of the pack to claim his 41st MotoGP victory, and his 62nd in Grand Prix motorcycle racing.
Moto3 had Romano Fenati of KTM begin from pole position and kept first place until teammate Brad Binder duelled him for the lead and Nicolò Bulega joined soon after.
All bikes featured unified electronic packages in an attempt to reduce costs, close the deficit between the factory and satellite teams and bring a new focus on rider control.
One of the main changes involved the début appearance of 2014 Moto2 World Champion Tito Rabat on one of the two Marc VDS Racing bikes.
[10] AB Motoracing and Karel Abraham left MotoGP after five seasons and switched to the Superbike World Championship as did Alex de Angelis and Ioda Racing.
[11][12] Loris Baz moved to Avintia Racing to replace Mike Di Meglio who went to the FIM Endurance World Championship.
[13][14] The final change was Stefan Bradl who remained with Aprilia after riding for them as a replacement rider in 2015 when Marco Melandri left MotoGP during the middle of the season.
He spoke of his satisfaction of adapting well to the Michelin tyres and knew a good position in Qatar would demonstrate his quick race pace, "I would like to start this 2016 season in the best way possible, especially compared to the beginning of 2015.
Bradley Smith was the only rider to crash in the session when he lost control of the front of his bike and fell at turn thirteen with two minutes left.
[26][27] Petrucci fractured three metacarpal bones in his right hand in a pre-season testing accident at Phillip Island Grand Prix Circuit.
[28] Petrucci was in pain after the third practice and underwent an x-ray which revealed a dislocated bone segment in his third metacarpal due to some fractures sealed by surgery re-opening under the stress of riding.
[29] Before Saturday's action started, a moment of silence was held for Tunisian motorcyclist Taoufik Gattouchi who died from injuries he sustained in a multi-bike accident in the Losail 600 Cup support race.
Márquez, Dovizioso, Rossi, Iannone, Crutchlow, Pol Espargaró, Viñales, Redding and Smith completed the top ten ahead of qualifying.
Rossi alleged Lorenzo did not notice him and likened the situation to the penalty point he received on his race licence after qualifying for the 2015 San Marino and Rimini's Coast Grand Prix when he was deemed to have impeded him.
[34] All riders ran twice with most entering the pit lane with five minutes left in the crash-free second qualifying session and pushed immediately due to optimum track conditions.
[35] On his first run in clear air, Lorenzo claimed a record-breaking, 62nd career pole position and his 36th in MotoGP with a time of one minute and 54.543 seconds but could not improve due to a rider error.
[36] Márquez executed a wheelie because his front tyre locked due to a possible brake malfunction and veered left into the gravel trap during a practice start.
Pedrosa took seventh having been unable to improve his position due to a problem with his second set of tyres and was ahead of Barberá's leading satellite bike.
Crutchlow progressed to the second session as its fastest driver and was tenth in front of Smith (who had little confidence with bike control in the corners) and Redding.
Rossi, Dovizioso, Iannone, Crutchlow, Redding, Pol Espargaró and Smith made up the rest of the top ten fastest riders.
[46][48][49] But, as Iannone was starting to get back at teammate Dovizioso for the lead, he ran onto the dirty white line at turn thirteen and lost control of the front of his bike.
"[55] Iannone explained that he reviewed the data after his lap six crash and said he was puzzled about how it caused him to retire, "Usually the white line has grip, but this time it's very, very slippery.
He said he could not have pushed harder earlier in the Grand Prix, "I was strong but not enough to try one attack, to have one sector, one braking, one part where I was a little bit faster than the guys in front of me.
"[57] Crutchlow said he was angry because he felt his bike had good pace and explained it grew increasingly out of sync as the race progressed because of his engine braking glitch that had reoccurred from practice.
Johann Zarco, Marcel Schrötter, Lowes and Rins were handed ride-through penalties because they were judged to have jumped the start and served them on the next lap.
Lüthi glimpsed space midway through the penultimate lap and began drawing closer to Morbidelli who narrowly held on for the rest of the race to win on the road.
[62] After the event, race director Mike Webb explained a camera that observes jump starts did not show the correct images because of a recording and playback fault.
Webb said he would speak to the Grand Prix Commission about reviewing the regulation on how penalties are applied within the opening four laps of the race to riders who are deemed to have jumped the start.
On lap nine, Binder took advantage of heavy fighting for the lead to claim the position, but Fenati caught him on the main straight and the duel continued.
Antonelli then moved out of the slipstream and successfully out-dragged Binder to clinch his third career Moto3 victory by seven-thousands of a second and became the early leader of the Riders' Championship.