The 29-year-old German was leading the sprinters' green jersey competition at the time he abandoned having won five stages so far.
"Another sad news: Green jersey @marcelkittel, and winner of five #TDF2017 stages, has stopped at the top of Col de la Croix de Fer," said the German's Quick-Step team on Twitter.
What had been a hugely successful Tour for Kittel quickly turned sour as he crashed 20km into Wednesday's stage.
He was cut and bloodied and even needed to change a shoe while hanging onto his team car as the race continued.
The peloton led by race leader Chris Froome's Team Sky sat up and waited for Kittel but once the climbing began with the second category Col d'Ornon, the German started to lose touch with the bunch.
By the 24km long hors category Col de la Croix de Fer just over 100km from the finish, he was losing serious ground and the prospect of getting to the finish line within the required time delay was diminishing, so Kittel quit.
"We might not have Paris, but we'll always have these fantastic wins! Thank you, @marcelkittel!" added Quick-Step.
Kittel had taken his personal total to 14 Tour stage wins, overtaking the record mark of 12 by a German that Erik Zabel managed.
He had held a 128-point lead over Michael Matthews in the green jersey competition and looked likely to win that.
But a determined Matthews had whittled down that lead to just 29 points over the past four days and by winning Wednesday's intermediate sprint, he moved to just nine points behind Kittel.
The German would still have been expected to win the jersey with two likely flat stage sprints to come but Matthews could have taken it off him on Thursday's stage with 20 points up for grab in the intermediate sprint there.
As it is, the Australian will now wear the green jersey on Thursday and with a 160-point lead over German Andre Greipel, he is almost certain to win it if he reaches Paris.
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