This was a positive day for Chris Froome as he earned back time lost in his stage-one crash, as well as an indication as to just how strong Porte's challenge could be once this race enters mountains, with such a reliable group surrounding the 33-year-old Australian - who himself played such an important role as domestique in Froome's early success.
Chris Froome'sTeam Sky finished just four seconds behind.
Germany's Team Sunweb finished fifth, 12 seconds behind winners BMC.
"I don't think it is a bad thing to have the yellow jersey for a team looking for a sponsor", said Porte, who crashed out of last year's Tour and lost time in Stage 1 of this edition.
Van Avermaet's teammate Tejay van Garderen finished on the same time to take second place overall with Sky's Geraint Thomas third. "To win the stage with a team like we have here, and especially with the passing of Andy Rihs, is special", Porte said.
"Obviously the (Tour) didn't start too well with the crash on stage one but that's bike racing".
Among Froome's main rivals, France's Romain Bardet lost 1:15 today and now trails the Briton by 20 seconds.
"We're taking some time back on some of the other GC guys", said Porte.
It was also a very satisfying day for Froome, the Kenyan-born Briton ignoring some booing at the start line and making up some of the valuable time he lost on Saturday's first stage. "It's a long way to go, we still have six more hectic days and then we have also got the Alps and the Pyrenees".
"This makes up for previous year", he said.
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.
The Belgian fans were quick to point out that one of their riders would be wearing the Tour de France yellow jersey on the day their team play France in football'sWorld Cup semi-finals.
The Tour remains in western France for Stage 3 on Monday with its first team time trial since 2015.
The Tour resumes tomorrow with the 195 km flat stage four that runs between La Baule and Sarzeau.