The 35.5km teams trial held in and around Cholet was a key test for the general classification favourites. It proved interesting with enough changes to the time gaps among riders like Porte, Chris Froome (Sky), Vincenzo Nibali (Bahrain-Merida) and Romain Bardet (AG2R) to make for a juicy race.
With the teams starting in the reverse order of the teams classification, it was Mitchelton-Scott who set the early benchmark, only to lose the top spot to Team Sky. The British squad were also early starters after crashes in Stage 1 set them back.
Sky had to plough their way through a torrent of boos from the fans lining the roadside, but still set an impressive time to displace Mitchelton-Scott as provisional leaders.
BMC also started early on, and leveraged a smooth performance out on the road into a superb time which overtook Team Sky at the finish.
There was then a long wait in the hot seat and at the end of the stage it was BMC won the stage, with four seconds lead over Sky and seven seconds over Quick-Step Floors.
“I think we were really smooth today," said van Avermaet. "I think everybody did a good time trial and we were all working well together.
"We knew that Team Sky would be the team to beat and we also knew that it would be close. We worked together and that’s what team time trials are about. We stayed together with eight guys for a long time and on this parcours, that was the key to winning the race.”
It will be van Avermaet's second stint in yellow after three days in the maillot jaune during the 2016 Tour de France.
“It was a goal to get yellow in the first week," said van Avermaet. "I have worn it one time already and it was an incredible feeling so, I am pretty happy to be in this position for a second time. I will enjoy it tomorrow because for any rider it is a special feeling."
It was also a important result for Australian general classification hopeful Richie Porte, who essentially erased the deficit he had sustained after getting caught behind a crash in Stage 1.
Mitchelton-Scott finished fourth after sitting on the hot seat until Sky bumped them off that perch. BMC then held the top position through to the end after it got the better of Sky.
BORA-hansgrohe finished their run last with Peter Sagan surrendering the leader's jersey to van Avermaet, swapping yellow his his ultimate target of green.
Movistar finished 53 seconds off the pace, placing its leaders in further deficit, including Nairo Quintana who is now over two minutes behind van Avermaet.
The other big loser of the day was Dan Martin and his UAE Team Emirates squad, with the Irishman losing a minute and 39 seconds to BMC.
Tejay van Garderen (BMC) follows his teammate Van Avermaet on the general classification while Sky's Geraint Thomas sits third.