Quick-Step Floors was one of the strongest teams of the day and finished the course in 38 minutes and 53 seconds, which meant that Greg Van Avermaet was to take the leader's jersey.
Vincenzo Nibali's Bahrain-Merida squad were 11th on the day, giving up 62 seconds to Sky, while Romain Bardet's AG2R La Mondiale team finished 12th, 71 seconds off Sky's time.
Overall, Froome is in 18th place, 55sec off the pace and still 44 behind 2017 Giro d'Italia victor Dutchman Tom Dumoulin, who with Team Sunweb only lost 7sec to the Briton. "It was a good sprint, slightly uphill in the end, but I had good legs and a good feeling", said Gaviria, only the second Colombian to wear the yellow jersey after Victor Hugo Pena in 2003.
Froome's misfortune is a boost for France's Romain Bardet, seen along with Quintana as the four-time champion's main rival in this year's race, and also for Dutchman Tom Dumoulin, the 2017 Giro d'Italia victor.
The main favourites for the Tour de France Christopher froome after three rounds loses the interim leader 55 seconds.
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The world champion profited from a mass crash that also involved the victor of stage one, Colombian Fernando Gaviria and another favourite Michael Matthews, some two kilometres before the finish. It would have been nice not to have lost it in the first place.
"There will be a lot more time lost throughout the GC group before we hit the mountains".
BMC's win on Monday, their third in a team time trial this year, had several positive outcomes.
"I still regret throwing away those 51 seconds on the first day, but there's a long way to go to Paris".
"It was a huge challenge for the team, it's been incredible for us", said the 33-year-old Briton who was jeered when his name was announced on the starting ramp.
Tonight's fourth stage is a flat, 195km stage in Brittany between La Baule and Sarzeau that is expected to finish in a bunch sprint.