The Swiss rider, who was 34th overall in the standings, has not suffered an injury, but has instead withdrawn so that he can rest up ahead of September's World Championships.
"I will travel home now and take a little break. The season has been long for me, starting back in Dubai," said the 33-year-old.
"I have done 59 days of competition this season so far and I have another big goal at the end of this season, the World Championships. It is not a secret that I would like to be in my best shape there, so it is important that I take some rest."
Cancellara has previously won eight stages of the Tour.