Froome's Team Sky were last out on the 28km route and finished in second, 0.62 seconds slower than BMC Racing.
The 2013 champion now leads BMC's American rider Tejay van Garderen by 12 seconds in the overall standings.
Froome gained more time on two-time winner Alberto Contador, Nairo Quintana and defending champion Vincenzo Nibali.
Italian Nibali was the day's biggest loser in the battle between the so called 'big four' with his Astana team finishing 35 seconds adrift of the winners. He now trails Froome by two minutes and 22 seconds.
"I am surprised he's lost so much time already," said Froome.
"I certainly didn't expect it. I thought he was going to be the one guy from the main contenders who would gain time in this first phase of the race.
"Nibali and Quintana have lost substantial time already so the pressure is on them to be attacking as we go into the climbs."
