The Quick-Step Floors rider had won five stages of this year's race to lead the green points jersey classification.
Kittel injured his right shoulder in the crash on a flat section of road, 20km into the stage.
Australia's Michael Matthews, who was nine points adrift, will take over the lead and hold a virtually unassailable 160-point advantage over Andre Greipel.
The points classification, which rewards consistently high finishes, had been providing a terrific sub-plot to the race.
World champion Peter Sagan had won the five previous green jerseys and was attempting to match Erik Zabel's record of six.
However, the Slovakian was disqualified from the race for causing Britain's Mark Cavendish to crash out on stage four.
That left Kittel, who is a pure sprinter, in the jersey and he built an advantage of more than 100 points over Matthews.
Team Sunweb rider Matthews is a better climber and can therefore pick up points at intermediate sprints on more mountainous stages - as he did on stage 17 - and he had whittled the lead down.
It would now appear as though Matthews just needs to stay on his bike to Paris to win the jersey.
There are 60 intermediate sprint points available plus 50 points for the winner of the 21st and final stage, which is likely to be a sprinter, such as Germany's Greipel.
However, Greipel will not be able to pick up any points in the mountain-top finish on stage 18, and is unlikely to win stage 20's individual time trial.
Germany's Marcel Kittel has abandoned the Tour de France after crashing on Wednesday's stage 17 in the Alps.