The Team Sky rider was brought down in a collision between riders and a parked motorcycle on the way to the first summit finish to Blockhaus, and despite finishing second in Tuesday's stage 10 time trial, says "each day has become a case of trying to survive each day rather than racing."
The Welshman sat 15th in general classification before stage 13, 6-46 down on leader Tom Dumoulin (Sunweb), but will now turn his attention to being fit for the Tour de France and aiding Chris Froome to a fourth victory.
“I’ve been suffering since my crash on Sunday," Geraint Thomas said in a statement on Friday. "I’ve had an issue with my shoulder which is manageable, but my knee has also been getting worse each day.
“Obviously it’s never nice to leave a race early, especially when it’s your main goal of the season, but I have to look at the bigger picture. I'd love to continue, but it would be a case of trying to survive each day rather than racing.
“I’ll turn my attention to the Tour now, and I want to arrive there with as good form as I started the Giro.
“I want to thank all the staff and riders here. It’s been great fun and I wish them all the best for the remainder of the Giro. I’ve really enjoyed racing in Italy again. The fans have been amazing and I’ll be back.”
It's another blow to Team Sky who have now tried on four occasions to land the top overall result at the Giro, with Bradley Wiggins, Richie Porte and Mikel Landa all abandoning in their recent attempts. Rigoberto Uran still holds the best result for Team Sky when he took second place behind Vincenzo Nibali after Wiggins had abandoned in 2013.
Like last year with Landa's abandonment, the team now say they will look for stage wins in the remaining days of the 100th edition. In 2016, Mikel Nieve salvaged some success with his stage win and taking the king of the mountains jersey.
“It’s desperately sad for Geraint," said Sky boss Dave Brailsford. "He has worked hard to arrive here in such great condition and we were looking forward to seeing him compete.
Watch: Giro d'Italia stages 16-21 preview
“As always, he has shown true fighting spirit and demonstrated what a competitor he is, but the impacts of a crash like that take their toll.
"We have to make sure that his injuries are managed optimally, ensure he is able to maintain his fitness and condition, and then look to set new targets.
“As far as the team goes, the GC has gone but there is still plenty to fight for and the opportunity is there for our riders to achieve a stage win in the 100th Giro”.
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