Alaphilippe, of the Quick Step team, launched an audacious lone attack on the third and penultimate climb and went on to solo over the finish several minutes ahead of the main peloton after a first day in the Alps marked by Van Avermaet outfoxing Team Sky in the yellow jersey stakes.
"It was a very hard rhythm all day long".
Froome is 3:21 behind Van Avermaet after recovering from a punctured tire atop the second of the stage's ascents, finishing with Thomas and most of the top contenders.
Thomas, of Team Sky, completed an impressive ride on the 108.5km stage from Albertville to the summit of La Rosiere by overtaking Spaniard Mikel Nieve (Mitchelton) in the closing metres.
That saw Van Avermaet extend his overall lead to two minutes and 22 seconds over Thomas, with Movistar's Alejandro Valverde up to third, three minutes and 10 seconds back.
"If people want to come out and boo, then that's fine".
Sky started this Tour de France featuring Froome as the leader, with Thomas given wildcard status after years of putting in loyal domestique work.
Froome is fresh from winning the Giro d'Italia and, having won the 2017 Tour of Spain and France, is targetting a fourth consecutive Grand Tour triumph and the first Giro d'Italia-Tour de France double since the 1998 feat of the late Marco Pantani of Italy. It cracked me up because I knew he was watching.
Oil trades below $69 as investors weigh mixed inventories report
US crude oil production last week hit 11 million barrels per day (bpd) for the first time in the nation's history. Holding production steady would mean shipping less crude than Saudi Arabia indicated after the Opec deal.
"We're still here to try and win the race, whatever way that is". For me, it's already a success. "I can have a super good day after a rest day and go over the limits but I pay it back..."
"I've been called a lot worse - on my Richter scale, that's not bad", he said.
Froome is attempting to match the record of five Tour victories shared by Jacques Anquetil, Merckx, Bernard Hinault and Miguel Indurain.
Nibali, victor of the Tour in 2014, was later forced to abandon the race with a fractured vertebra. I committed, got across to Dumoulin and then sat on. It's just a bit of an unknown for me to race over three weeks.
"Both riders were spat at, Froome was shoved, shorts were dropped in their direction", reports Jeremy Whittle in The Guardian, "yet it was Vincenzo Nibali who ended up prone on the tarmac, after tangling with spectators, as the leaders were blinded by smoke from flares".
But it was the yellow jersey wearer who pulled away to win the iconic Alpe d'Huez stage, delivering another emphatic statement of his General Classification credentials as he extended his lead over Froome to one minute and 39 seconds. "But he has no references in a three-week race so we can always speculate on that", said Lavenu. "When they go, it is never nice to see them all riding away but we had confidence in each other and we rode really well". Jakob Fuglsang of Astana was next at 3:12.
The rider leading at the end of the first mountain stage has gone on to win the Tour every year since 2012 but Van Avermaet knows he will bring that sequence to an end.
The 158.5-kilometer (98.5-mile) from Lake Annecy incorporated climbs over four major Alpine passes before the final descent sprinting to the finish at Le Grand Bornand.