Less than 30 kilometers into the stage, a protest by French farmers brought to the riders to a halt after bales of hay were thrown onto the road.
Police then used a spray to tackle some of the protesters as the race approached, and it appeared to get into the eyes of a number of riders.
It took 15 minutes for officials to treat riders and clear the area before the race resumed.
The race continued after the brief hiatus.
Stage 16 was eventually won by Quick-Step's French rider Julian Alaphilippe, who profited from Adam Yates' fall on the final descent to claim his second stage win of Le Tour 2018.
The Tour de France thinks it has some solutions to liven up the action: Shorter mountain stages, sprints for bonus seconds and a Formula One-like grid start.
1 killed, 13 injured in shooting in Toronto, gunman dead
Toronto Mayor John Tory told reporters that the city has a gun problem and guns were too readily available to too many people. John Tulloch said he and his brother had just gotten out of their auto on Danforth when he heard about 20 to 30 gunshots.
The stage resumed after a 15-minute interruption and Alaphilippe stayed quiet in the breakaway group until the last climb to the Col du Portillon.
Belgian cyclist Philippe Gilbert posted an image online of his leg following the race, and we mean it when we say it is truly disgusting.
Thomas still leads his Team Sky mate and defending champion Chris Froome by 1 minute, 39 seconds and Dutchman Tom Dumoulin by 1 minutes, 50 seconds going into Wednesday's 17th stage, a brutal 65-km, up-and-down trek from Bagneres-de-Luchon to Saint-Lary-Soulan.
"I crashed and it was all my fault". It was fortunate they were only tossing hay bales into the road.
Should he gain time on Thomas, the world time trial champion could still pip the Team Sky duo in Saturday's solo effort against the clock.
"I knew the last kilometres of the stage".
Yates was quickly back on his bike, and followed home Bahrain-Merida's Gorka Izagirre to finish third.