Valverde, third overall in 2015, skidded into a safety barrier after losing control of his bike on a wet left-hand corner on the 14-km course in Duesseldorf.
The 37-year-old was treated by race medics on the spot before being taken to hospital.
His team, Movistar, said that Valverde, who made an excellent start to the season with victories in the Liege-Bastogne-Liege classic and the Tour of Catalonia, had been forced to abandon with a broken knee cap.
"At first we thought it was just a crash, like happens often, but when we saw that he could not get up, we knew it was serious," said sports director Jose Vicente Garcia.
"It is a sad day for us."
Valverde and Quintana were seen as a formidable double act on this Tour, but the Colombian, second overall in 2013 and 2015, will now have to make do without the help of the Spanish veteran.
"It's really difficult for all of us - he's a very important person and a great team mate. I just hope it's nothing really serious. It's awful to see his race ending that way, so early," said Quintana.
(Reporting by Julien Pretot; Editing by Toby Davis, Neville Dalton)
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