Team Sky had laid down the gauntlet with a strong effort, but having recorded an identical time over the first 13 kilometres, BMC were six seconds ahead as they passed through the second checkpoint.
Porte may be linked with a switch to the American Trek-Segafredo team next year, but the future of other riders and team staff is uncertain; and in the biggest race of the year, Monday's victory was the medicine they all collectively needed to reaffirm their overriding goal of reaching the finish as the team of the 2018 Tour victor.
La Roche-sur-Yon, France (AFP) - World champion Peter Sagan said he had three reasons to be cheerful as he won stage two and took the overall leader's yellow jersey in front of family and friends from Slovakia on the Tour de France on Sunday.
With Froome, Yates and BMC's Richie Porte three of the four big losers among the general classification riders on Saturday, this stage did much to level the playing field. I think there will be a lot more time lost throughout the GC group before we hit the mountains.
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.
"I'm happy to be here", Froome noted.
Overall, Froome is in 18th place, 55 seconds off the pace and still 44 behind 2017 Giro d'Italia victor Dutchman Tom Dumoulin, who with Team Sunweb only lost seven seconds to the Briton today. "We gave it everything we had and it all went pretty much to plan".
"I'll be wearing the yellow jersey probably for only one day, but I'm happy for that".
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"Our aim was to take the maximum time out of all our rivals", he insisted.
BMC Racing were the fifth team to start the stage and they laid down the marker early, edging other leading contenders Team Sky (38:50) and Mitchelton-Scott (38:55), to land themselves in the hot seat.
"We rode out of our skin and super smooth and with the horsepower that we have did a great ride", the Irishman said.
"It puts us right back in the game".
"We knew it was OK to lose Luke and Wout", Thomas said. To win with these guys is a great feeling.
"We were favourites and it was good to deliver".
Fernando Gaviria could have been donning the yellow jersey had Quick-Step Floors won the stage.
Among the big losers today were Nairo Quintana, whose Movistar team came home 53 seconds down on BMC Racing, Bahrain-Merida with 2014 Tour de France victor Vincenzo Nibali, 1 minute and 6 seconds down, and Romain Bardet's AG2R-La Mondiale, who came home 1 minute 15 seconds behind the day's victor.
Mark Cavendish's hopes of a 31st career Tour stage win were also scuppered by the incident but the Dimension Data rider stayed upright. Once the three were away, the main pack closed ranks to ensure that no other riders could join the break.