On a miserable, rain-sodden day in northern France, the Briton appeared in great pain after falling for the second time, some 70 kilometres from the finish.
The Team Sky rider stood holding the wrist he injured in another spill on Tuesday, and was limping heavily as he eventually climbed into a team vehicle after chatting to team doctor Alan Farrell and sports director Nicolas Portal.
"I'm obviously hugely disappointed," Froome said later.
"The way my hand was and the conditions, it was impossible to control my bike."
Earlier in the stage, a 152.5-km ride from Ypres, Belgium, Froome suffered his second crash in two days.
Froome hurt his wrist and suffered bruises to his left side in a fall on stage four but was cleared to start Wednesday's stage which featured several treacherous cobbled sectors.
The earlier fall on Wednesday was not too bad and he was helped back into the main bunch by his Sky team mates, but the second accident of the day proved one too many for his battered and bruised body.
The 29-year-old's build-up to the race was hardly ideal after a heavy crash last month on the Criterium du Dauphine.
Froome is the second high-profile rider to quit this year's Tour after fellow Briton Mark Cavendish suffered a high-speed crash in Saturday's opening stage bunch sprint in Harrogate.
Cavendish, winner of 25 Tour stages, underwent shoulder surgery on Wednesday as a result of the crash.
Froome's departure meant Australian Richie Porte will now assume the leader's role in the team.
"Given his fall yesterday, it was always going to be hard for Froomey to hang in there, so the decision was made on the bus that I'd have G (Geraint Thomas) and Bernie (Eisel) to ride for me, and they did an incredible job on the wet and slippery roads," Porte said.
"It was carnage before we even reached the cobbles, and I went down after the second sector myself, but fortunately I only had a few minor grazes."
Organisers announced before the start of Wednesday's stage that two of the nine cobbled sectors had been removed from the stage because of the bad weather conditions but crashes still littered the route.
(Editing by Martyn Herman)
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