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 on Monday.
Defending champion Chris Froome, who fell into a ditch near the end of Saturday's Stage 1, arrived safely with most of the peloton.
Mitchelton-Scott were fourth in the time trial, two seconds ahead of world champions Sunweb.
"I've had it before and you feel how big it is", Van Avermaet said. "To win the stage with a team like we have here, and especially with the passing of Andy Rihs, is special", Porte said.
Recovering sufficiently to finish one minute behind the Colombian victor, Fernando Gaviria, Froome ended up in the wrong position of a chaotic finish to a largely sedate first stage.
Dimension Data have been widely linked to Van Avermaet in the media, especially after he took the yellow jersey at the Tour de France, with L'Equipe suggesting that bike brand BMC will join the African team as a jersey sponsor and so help cover the costs of Van Avermaet's significant salary.
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But Gaviria was involved in a group pileup inside the three-kilometre zone that neutralizes the impact of accidents and could do nothing to stop Sagan from claiming a six-second overall lead.
The team time-trial might not be the opening week Tour staple it once was, but after the bruising high-octane action of the opening weekend, it represented a major chance for the GC contenders to make some major time gains - or claw back lost time - over their rivals. "I'm very happy with the other riders". Teammate Geraint Thomas is also a co-leader of the squad and sits third overall, just three seconds off yellow.
Squad leaders traded turns on the front of the team "trains", with the ability to constantly maintain a fast pace the decisive factor over a challenging - if not highly technical - route featuring a few minor hills. Despite being cleared of doping allegations on Monday, some skeptical fans have jeered the Kenyan-born British rider since his Sky team arrived in France.
Thomas, who wore yellow for four days previous year, said that he was not bothered by the...
"I feel maybe even better (than last year)", Porte said.
Van Avermaet also wore the yellow jersey for three days on the 2016 Tour.
Cavendish, looking to add to his 30 career Tour stage wins and chase down Eddy Merckx's all-time record of 34, was well-placed with his Dimension Data team in the long straight to the finish line in Sarzeau on Brittany's west coast.