The team sent Simon Yates home on the rest day, and lost Mat Hayman on stage 10.
Gerrans, who in the 2013 Tour de France wore the maillot jaune of overall race leader following the team time trial, has been suffering since the crash in the opening stage of this year's race in Harrogate, where he collided with Mark Cavendish (Omega Pharma-Quickstep).
The 34-year-old will now head home to recover and ramp up for the goals of the second half of the season.
"Obviously it’s disappointing not to complete the Tour de France and make it to Paris," Gerrans said. "But with the injuries I have from stage one I think the best decision is actually to stop now and completely recover.
"I know I haven’t been 100 per cent right since my crash but I was hoping to improve throughout the race. That hasn't really been the case so I have been putting on a brave face and doing what I can each day."
The winner of Liège-Bastogne-Liège decided that racing through the Pyrenees into Paris was not the best way to recover, and his team agreed.
"Obviously everyone is aware that Simon injured himself quite badly on stage one," team director Matt White said.
"He has done very well to get this far in the Tour and give it his all on numerous days for the team to try and get some results, but he is clearly not at 100 per cent.
"The only way he is going to regain his full fitness, his full health, is to go home and have a rest. He is not going to recover finishing off these last few days."