Chris Froome's Team Sky came up four seconds short of BMC, as Greg Van Avermaet claimed the yellow jersey.
Team Sky (38:50) were second fastest to help four-time victor Froome climb the standings, with Quick-Step Floors another three seconds adrift in third.
Porte may be linked with a switch to the American Trek-Segafredo team next year, but the future of other riders and team staff is uncertain; and in the biggest race of the year, Monday's victory was the medicine they all collectively needed to reaffirm their overriding goal of reaching the finish as the team of the 2018 Tour victor.
The world champion held off a strong challenge from Italian Sonny Colbrelli to clinch the stage and take the yellow jersey from Fernando Gaviria, who was one of the late crash victims.
Porte's BMC team had been expected to make up for their disappointing first day when their Australian leader fell.
Froome, hoping to become the first rider in 20 years to achieve a Giro-Tour double, crashed into a grass section on the side of the road with five kilometres left and was quickly back on his bike, but the speeding peloton did not wait as preparations for the final mass sprint had started.
France determined to defeat Henry's Belgium
A living legend of French football, Henry was one of the stars during their 1998 World Cup win. Vermaelen believes France will be tougher opponents than five-times world champions Brazil.
And though Sky missed out on victory - and a chance to put Geraint Thomas in the yellow jersey - Froome was able to eradicate the deficit to numerous other contenders.
Other riders suffered here, like French favourite Romain Bardet who lost significant time with Ag2r La Mondiale of more than a minute, and Movistar and Quintana who gave up 53 seconds.
"I still regret throwing away those 51 seconds on the first day, but there's a long way to go to Paris".
BMC, which was planning to win back some time for Richie Porte, was the next team to set the best time.
Thomas, who wore yellow for four days previous year, said that he was not bothered by the...
"But this is the biggest one in the world and you get to stand up there on the podium with your team-mates and having a team-mate jump into the yellow jersey is another cool aspect", Bevin said.
The International Cycling Union WorldTour race is due to continue tomorrow with a 195km stage from La Baule to Sarzeau.