The gritty Belgian, who won the partially cobbled Paris Roubaix monument race in April, came first on three stages and twice on two to win by 29sec from Xandro Meurisse and 36sec on third placed Anthony Perez.
"I'm still not quite at the top of my form," said the 32-year-old who will be helping BMC co-leaders Richie Porte and Tejay van Garderen in next month's Tour de France.
"I want to win a stage on the Tour this year," said Van Avermaet, who won stages in both 2015 and 2016 and will be relishing a Tour packed with opportunities for a powerful puncher of his stature.
