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.
The Briton crossed the line 51 seconds behind Tour debutant Gaviria, who won a bunch sprint after the 201km ride from Noirmoutier-en-l'Ile ahead of world champion Peter Sagan and German Marcel Kittel, second and third respectively.
"It’s an incredible day, I want to thank my team mates. 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.
Fellow Colombian Quintana, twice a Tour runner-up, suffered a puncture 3.5 km from the line and finished one minute 15 seconds off the pace.
Other top contenders Briton Adam Yates and Australian Richie Porte also lost 51 seconds after being involved in pile-ups.
In a race that could be decided by a matter of seconds, the time loss is a big early setback for Team Sky leader Froome, in the race after being cleared of any wrongdoing following a urine test that showed he had an excessive level of a banned asthma medication in last year’s Tour of Spain.
He will have an opportunity to make up for it in Monday’s team time trial in Cholet, although he was expected to gain ground on his rivals in the collective effort against the clock, not just cancel out lost time.
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 winner.
Separately, France’s Sylvain Chavanel, who wore the yellow jersey in 2010, became the first rider to start 18 Tours de France.
(Reporting by Julien Pretot; Editing by Hugh Lawson)
