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.

The Institute for Economics and Peace published its Global Peace Index on Thursday for the 11th year running.
Researchers said conflict costs had an enormous impact on economies worldwide.
They called for more money to be spent on peace building.
Their report found that the world became 0.28% more peaceful over the past year.
This was driven by a drop in state-sponsored violence, including torture and extrajudicial killings, and a decrease in the murder rate. The delayed effect of the US and UK withdrawing troops from Afghanistan also made itself felt in the research.
But the overall trend was not borne out inside the US, where an increase in murders and a higher level of perceived crime pushed peacefulness down.
And while terrorism levels jumped in Europe, it remained the most peaceful region on the planet.
The number of countries seeing a record number of deaths from terrorism rose to 23. Among those were Denmark, Sweden, France and Turkey. Researchers found that 60% of countries now have a higher rate of terrorism than they did 10 years ago.
The research did not cover the time period of the attack on Manchester in the UK last month.
Increased support for populism in Europe corresponded with a deterioration in peacefulness levels, the report suggested, as wealth inequality rises, media freedoms decrease and people's acceptance of the rights of others diminishes.
In Colombia, the ceasefire between the Farc armed group and the government was reflected in improved scores, notably in the number of deaths from internal conflict, but the country's peacefulness score was held back by ongoing activity by a smaller armed group, the ELN.
Researchers used a multifaceted index of peace indicators - they measured the homicide rate, the ease of access to weapons, the impact of terrorism and the number of armed services personnel in the population, among other things.
Syria is the least peaceful country in the world for the fifth year running. Before the outbreak of civil war there, it was the 65th least peaceful. Its fall has been the starkest of the past decade.
The other four most violent countries are Afghanistan, Iraq, South Sudan, and Yemen.
The combined Middle East and North Africa was the least peaceful region in the world.
Iceland remained the most peaceful country in the world, a spot it has occupied since 2008.
The other four most peaceful countries are New Zealand, Portugal, Austria, and Denmark.
Germany's Marcel Kittel has abandoned the Tour de France after crashing on Wednesday's stage 17 in the Alps.
[NEXT_CONCEPT]
Levels of peace around the world have improved slightly for the first time since the Syrian war began, but harmony has decreased in the US and terrorism records have increased, a Sydney-based think-tank has found.