The Olympic and Tour de France champion did not take to the start for stage six - a 190km trek from Powis Castle in Welshpool to Caerphilly Castle.
"I'm sorry to have to pull out of the Tour," Wiggins told the Team Sky website.
"I've loved the last six days, meeting so many people around the country and enjoying those crowds along the roads. It has been a great experience, but this bug sadly means I'll now miss the climax this weekend.
"I'm sorry I can't continue and would like to thank all those fans, of all ages, for the support."
The Team Sky rider saw his hopes of overall victory end on Thursday when he dropped out of the lead group to help Mark Cavendish.
The Olympic time trial champion eventually finished 11:45 behind stage winner Marc de Maar.
The race finishes on Sunday in Guildford.