"You can boo, be vocal, but don't affect the race", said Thomas.
Twice an Olympic gold medal victor on the track, Thomas now leads his team leader by one minute and 39 seconds, with Dumoulin a further 11 seconds back.
Nibali, who claimed his sole yellow jersey in 2014, was transported to hospital with a suspected vertebra fracture after coming down hard following the collision.
In the end, Van Avermaet produced a fantastic performance to finish 1min 43secs behind Alaphilippe, Thomas, Froome and Team Sky trailing over the finish over three minutes behind the stage victor.
While there was no drama for Thomas in racing terms, there was an incident inside the final 20 kilometres when a spectator appeared to throw a lit flare into the peloton, close to head height for the passing Sky riders who were on that side of the road, though all of the riders passed safely.
Rigoberto Uran, who finished second overall previous year, did not start the stage as the effects of a stage nine crash caught up with him.
"Don't touch the riders, don't spit at us". "There were two police motorbikes, but no barriers at that point", the Italian said.
Marshalltown Hospital Closed Due to Tornado Damage
National Weather Service meteorologist Rod Donavon said two primary storms spawned the series of damaging tornadoes. According to CNN affiliate WOI , another tornado damaged houses in Bondurant, about 15km from Des Moines.
On Stage 12, Dumoulin was able to endure the attacks from the likes of Froome, Bardet, Quintana, Nibali and Landa, attacking the regrouped GC bunch to finish second just two seconds behind Thomas.
Froome also courted boos and jeers from the crowds, while there were audible boos as Thomas took to the podium to celebrate his stage win.
The four-time Tour victor briefly turned to remonstrate with the man who hit out at him with about 7 kilometres to go, but will be happy to have made it up safely.
Though Froome saw his deficit to yellow grow, he called Thomas' lead a "dream position" for Sky.
"Obviously Froomey is the leader".
While it was another day of triumph for the Welshman, the sprinters labored once more, with Andre Greipel, Dylan Groenewegen and Fernando Gaviria dropping out.
Dutchman Steven Kruijswijk, who was a threat in the general classification, opened up a six-minute lead with an early attack but Sky never panicked and their Colombian prodigy Egan Bernal did an awe-inspiring job on the final ascent to rein in the Lotto-Jumbo NL rider.
Rigoberto Uran, last year's runner-up, withdrew before the stage began, having failed to recover from a crash on the cobblestones in Stage 9. He's got a strong time trial so the favourites won't want to give him a long leash, but he's still unproven as a leader over three weeks.