The Belgian leads the standings in 9:08:55 after the team finished the 35km race against the clock in 38:46. His teammate Tejay van Garderen lies second overall in the same time.
Britain’s Geraint Thomas is third overall, three seconds behind Van Avermaet, after Team Sky placed second in 38:50.
Belgium’s Philippe Gilbert moved up to fourth thanks to Quick-Step Floors’ ride of 38:53, which gave them third on the stage.
Overnight leader Peter Sagan moved to 80th overall, three minutes behind Van Avermaet, after Bora-Hansgrohe placed seventh on the day. He remains in the green jersey and will wear it for the first time tomorrow after he secured the lead in the points competition on stage two.
Sunweb’s Tom Dumoulin, who placed second in the Giro d’Italia and is seen as one of Chris Froome’s major challenges, moved into seventh (11 seconds behind) after a respectable ride by his team. Froome moved into 18th (55 seconds off the pace).
Mitchelton-Scott’s Daryl Impey, 21st overall at one minute, is the first South African, one place behind his team leader and outside favourite Adam Yates.
Van Avermaet said afterwards that a team time-trial was always something special.
“The whole team does the effort for one goal in winning the stage and I think our team are masters in it.”
He added that it was a big goal to get yellow for the team in the first week.
“For a rider, it is something special. I want to thank my teammates because without them it would not have happened.”