His American BMC team got round the 35 and a half kilometre course four seconds faster than Team Sky.
The Tour de France has a new leader.
Belgian rider Belgian Greg van Avermaet won stage three and took the yellow jersey after winning the time trial in Cholet.
His American BMC team got round the 35.5 kilometre course four seconds faster than Team Sky and their formidable four time tour winner Chris Froome.
But the defending champion made inroads into his time lag of 51 seconds after crashing in stage one.
In the general classifications T J Van Garderden is second and Team Sky's Geraint Thomas is just three seconds behind in third.
Overall, Froome is in 18th place, 55 seconds off the pace and still 44 behind 2017 Giro d'Italia winner Dutchman Tom Dumoulin, who with Team Sunweb only lost seven seconds to the Briton on Monday.
Among the top contenders, last year's runner-up Rigoberto Uran of Colombia is 10th, 35 seconds behind.
Froome's Sky team mate Geraint Thomas could however prove a thorn in his side as the Welshman, who underlined his credentials by winning the Criterium du Dauphine last month, is third overall, 52 seconds ahead of his leader.
Tuesday's stage sees the tour take on 195 kilometres from La Baule to Sarzeu through flat terrain that will end in a sprint finish.