Both of Quintana's wheels due to speed bump with 3.5km to go. He stopped, received help from Mavic neutral support and stopped again to get his spare bike before arriving at the finish in Fontenay-Le-Comte.
"I hit a speed bump right before of the safety zone of the last three kilometres," Quintana said.
In the last three kilometres, the race jury allows riders to not lose time in case of a mechanical. Quintana was just outside of that limit and could not rely on the rule.
"Both of my wheels broke and I couldn't go on. This is how things work in cycling, there is no other way forward and it's only comforting that Chris Froome also lost time and so that means I'm only a few seconds behind him."
Froome lost time due to a crash at five kilometres to go. He rolled over the line 51 seconds behind stage winner Fernando Gaviria (Quick-Step Floors). Adam Yates (Mitchelton-Scott) and Richie Porte (BMC Racing), also held up in the crashes, finished with Froome. Quintana was further back while his fellow Colombian Gaviria celebrated stage victory.
Movistar are the only team to have brought three classification leaders to the 2018 race with Quintana, Mikel Landa and Alejandro Valverde. Landa called it "a catastrophe" for the Spanish WorldTour team and his team-mate.
"The first three quarters of the day were calm, but in the end came tension and nerves," Landa said. "It was very difficult. In such circumstances you never think, and it costs energy."
Quintana has twice finished second overall behind Froome in the Tour de France, and has taken victory in both the Giro d'Italia and Vuelta a España. Now he is fighting with Froome on the back foot after the first of 21 days of this 2018 edition.
"Although it is not the best way to start the Tour, there are many stages to try to recover time. And at least Alejandro and Landa finished with the lead group," team boss Eusebio Unzué said.
"We had Rojas, who was in charge of giving him his bike if any mishap occurred, but he fell beforehand. Soler was already off the back, and Amador and Bennati tried to help him later."
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