The Yamaha rider’s session ended moments after he was the fastest when he suffered an off-throttle highside in the Vale left-hander while riding on the hard rear tire.
Quartararo was slow to get to his feet and first had to be helped away by the marshals as he was struggling to put strain on his left ankle – although he was soon able to walk unaided and find his way back to his Yamaha garage.
The morning’s cloudy conditions persisted for the 45-minute FP2 session, but the increase in grip on the track meant the combined lap times could improve rapidly.
Aprilia’s Aleix Espargaro set the early pace with 2: 02.484 minutes before Quartararo was ahead with 2: 02.447 minutes.
As Quartararo’s dramas unfolded, Aleix Espargaro managed to set a record of 2: 00.670 minutes on Friday before improving to 2: 00.467 minutes.
Quartararo resumed the session on his second motorcycle with a little more than 20 minutes remaining and soon lit up the time windows even though he had ridden a soft front tire with more than 20 laps.
Quartararo again took the lead with 2: 00.138 seconds on a fresh middle rear end and improved to 2: 00.132 seconds with just over 10 minutes of the session before returning to the pit lane.
In the final moments Quartararo’s lap time was in jeopardy as most of the grid was fitted with fresh soft rubber for a time attack.
But Quartararo would put himself far out of reach with his penultimate flying lap, the Yamaha rider was eight tenths ahead of the field with 1: 59.317 minutes.
He would go unchallenged when the checkered flag fell, with Ducati’s Jack Miller as his closest rival in second place – albeit 0.512 seconds back.
Jack Miller, Ducati team
Photo by: Gold and Goose / Motorsport Images
The Styrian GP winner Jorge Martin stormed into third place late on his Pramac Ducati, Pol Espargaro led Honda team-mate Marc Marquez and completed the top 5.
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Francesco Bagnaia finished sixth on his factory Ducati after a frustrated Aleix Espargaro who had blocked his final flying lap by his brother Pol in the Stowe right-hander.
Brad Binder from KTM significantly improved the lap time in FP2 to 2: 00.315 minutes and finished the day in eighth ahead of Suzuki’s Alex Rins and Valentino Rossi on the Petronas SRT Yamaha.
Reigning world champion Joan Mir finished 13th as he continued learning the Silverstone track, followed by Johann Zarco on the Pramac Ducati.
Cal Crutchlow finished 16th on the works Yamaha, while his British compatriot Jake Dixon was 21st on the two year old SRT Yamaha, who found 1.3 seconds in his FP1 time this afternoon.
Lorenzo Savadori continues to struggle with his broken ankle on the Aprilia, which ended last Friday and was 5.8 seconds off pace.