And though Van Avermaet's BMC squad pipped Sky to victory by four seconds - denying Thomas yellow by just three seconds - Sky did enough to put four-time victor Froome firmly back in the general classification mix.
The Taupo rider Patrick Bevan has helped his American outfit BMC Racing to victory on the third stage, a 35.5km team time trial.
The stage three team time trial in Cholet, the location of the UAE hotel in these days, covers the same 35km distance.
Van Avermaet, a Belgian who excels at single-day classics and won the Rio Olympic road race, isn't a threat for the overall title but he could keep the lead through the cobblestoned Stage 9 ending in Roubaix.
Attention then turned to their rivals, with the biggest early losers including Movistar - who lost 53 seconds to BMC Racing and 49 to Team Sky, virtually cancelling out the time lost by Richie Porte and Chris Froome after the crashes that marred the stage one finale.More news: Drake Replaces DJ Khaled at Wireless Festival in London
On a sunny Saturday early in the school holidays, enormous crowds of fans packed the seaside towns along the Atlantic coast in a highly festive atmosphere where any expected fall out from the Froome booing on Thursday was muted, with AFP seeing just two signs along the roadside targeting him with messages of "Froome go home" and "Froome the doper".
Vincenzo Nibali's Bahrain-Merida squad were 11th on the day, giving up 62 seconds to Sky, while Romain Bardet's AG2R La Mondiale team finished 12th, 71 seconds off Sky's time.
"It's a dream. We rode a good time trial and the whole team worked hard", said Van Avermaet.
"It puts us right back in the game".
German Marcel Kittel, who has 14 Tour stage wins under his belt, suffered a puncture just under eight kilometres from the line and could not make it back to the front of the bunch in time. "You have to step up and deliver on the day and that's not an easy thing to do on a Tour de France team time trial stage".More news: UCLA's Billy Knight Allegedly Sexually Abused 9-Year-Old Girl Before Death
"In the last two kilometres I said "go" because I had good legs".
Sky finished second and Quick-Step Floors came third, seven seconds behind.
After Froome was waved off at the start in Noirmoutier-en-l'Ile by Eddy Merckx - one of the four men with five Tour titles to his name alongside Bernard Hinault, Jacques Anquetil and Miguel Indurain - the peloton enjoyed a fairly sedate ride through the Vendee, at least for 190km.
"It's been a great little journey over the past couple of months to come to this team and become part of a really tight team time trial unit and to really add to that is something I will be proud of for a long time", he said.
"There was way too much wind for me", said the slightly-built Porte. "I am a lot happier than I was at the Dauphiné, we have a gelled unit here and a powerful one".More news: Trump administration threatens tariffs on another $200 billion in Chinese imports
"You probably won't believe me but I didn't even think about it", he said of yellow. We just wanted to get that stage. "We had a clear plan and we're happy because we pulled it off".
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