Peter Sagan, the three-time defending world champion and three-time stage victor in this year's race, crashed on the descent from the Col de Val Louron, the second mountain of the day.
Motorbikes aren't controlled by any partisan interests, normally they are driven by Tour de France staff and are ferrying photographers and TV cameras and so rarely attract time penalties for drafting.
Despite not being able to get a gap on the Aubisque uphill, Roglič continued to attack on the descent into Laurens, eventually obtaining a gap that he was able to extend all the way into the finish, winning the stage by 19 seconds. "I will try to test Thomas". We could see a few crashes that cull the peloton further prior to the final weekend.
A member of the Gendarme caused the two men to stop abruptly and crash before he then pulled Chris Froome off his bicycle.
With so much climbing to do right from the start, riders warmed up for up to an hour both on the road and on stationary rollers before the stage started.
"It's fantastic. I'm really happy", added Alaphilippe, who also had some kind words for teammate Philippe Gilbert. "I thought of him a lot".
Gutsy Gilbert survives spectacular crash on Tour
Police were said to be arresting some protesters after farmers threw hay bales across the road before the peloton's arrival. This stage was just 65km long, but featured three towering climbs between Bagneres-de-Luchon and Col de Portet.
Pacing by motorbikes is a contentious issue within cycling, with Dan Martin (UAE Team Emirates) claiming earlier in the race that the peloton chasing him had been the beneficiaries of a motorbike, which had helped the main bunch bring him back after an attack on Stage 15. Dumoulin was trying to catch up after losing time due to a broken wheel. The time trial on Saturday will be fine.
Safe in the knowledge Quintana was unlikely to claw back his overnight deficit of almost four minutes, Sky let the Colombian go.
Froome finished eighth, one minutes 35 seconds behind, and dropped from second to third overall, a distant two minutes, 31 seconds behind Thomas, the Welsh rider seeking his first grand-tour victory.
Dumoulin, the defending world time trial champion and last year's Giro d'Italia victor, praised an otherwise impressive performance by Roglic.
The former world champion completed the stage - but it was later revealed he had fractured his kneecap.
But Thomas' lead is so comfortable, Dumoulin will have to launch a successful attack on Friday, or hope for an unlikely collapse from Thomas. "But when I got back to the hotel and was showed the pictures it was obviously something else".
Yesterday morning, Greipel wrote: "My apology go out to @ArnaudDemare and @GroupamaFDJ as I have had not the right to make that tweet based on Global Positioning System time, which can be wrong, plus I got the incorrect times he lost on the last hill".