The French Team DSM rider was sitting in a good position in the general classification, at just under a minute to the now former leader Rein Taaramäe (Intermarché-Wanty-Gobert Matériaux), who also lost time in the fall.
Bardet finished 180th on the stage alongside Ben Zwiehoff (Bora-Hansgrohe) and Mikel Nieve (BikeExchange), who also both came down hard. They all lost 12-32 to the peloton that was led in by Belgian sprinter Jasper Philipsen (Alpecin-Fenix).
A statement from Team DSM said: "After the final rider was brought back into the peloton with 15k kilometres to race the pace continued to rise and the peloton remained nervous.
"A touch of wheels near the front of the peloton saw a large number of riders hit the deck with just over 10 kilometres left, including Bardet who received checks on the road before continuing to finish some time down on his team-mate [Alberto] Dainese at the front of the race."
Bardet is now in 93rd place overall, 13-32 down on the frontrunners.
Team sports director, Matt Winston spoke briefly to Eurosport after the stage: "We never want to crash. It was a shame but we're happy we have Dyneema in our kit because, once again, it saved the majority of the injuries and he was able to come through.
"He's got a little bit of pain but definitely the Dyneema once again saved us - We don't know the extent of the injury [to his knee] yet."
Dyneema is a protective jersey and shorts used by the team that is designed to not break on impact with the road and to protect riders when involved in crashes, particularly protecting the arms, side and legs..
This is a disappointing crash for Bardet and the team who looked to be in a good position with Bardet, after an unusually good time trial in the opening stage followed by a solid enough ride on the first climbing day on stage three.
The French climber also came in with form after winning a stage and holding the leader's jersey for a couple of days at the recent Vuelta a Burgos, a week before this race.
The extent of Bardet's injuries are not yet known, but if he is still fit to ride the team now has a great option to go for stage wins in the huge amount of massive mountain stages that are yet to come in this Grand Tour.
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