The British rider withdrew before the 13th stage of the Giro d'Italia two weeks ago due to a chest infection and has not been able to train properly. Team Sky said Friday that Wiggins also has "an ongoing knee condition," and would not be included in the squad for the Tour.
"It's a huge disappointment not to make the Tour. I desperately wanted be there, for the team and for all the fans along the way — but it's not going to happen," Wiggins said in a team statement. "I can't train the way I need to train and I'm not going to be ready. Once you accept that, it's almost a relief not having to worry about the injury and the race against time."
Wiggins became the first British rider to win the Tour last year. In an astonishingly successful season, he also won the Paris-Nice stage race, Tour de Romandie, the Dauphine Libere and took Olympic gold in dominant fashion in the time trial.
"It's a big loss but, given these circumstances, we won't consider him for selection," Sky's team principal Dave Brailsford said. "It's incredibly sad to have the reigning champion at Team Sky but not lining up at the Tour. But he's a champion, a formidable athlete and will come back winning as he has before."
With Wiggins out, last year's runner-up Froome will become the undisputed team leader when the race starts on June 29. Sky had already said that Froome would be its team leader at this year's Tour, although Wiggins had indicated that he may have tried to ride for victory if he was in contention toward the end of the race.
Relations between the two were frosty during last year's Tour, with the 28-year-old Froome sometimes looking much the stronger rider in the climbs but being thwarted by team orders to support Wiggins rather than try and attack him.
This started off a spat between Wiggins' wife and Froome's girlfriend, as they took to show support for their partners by exchanging barbs on Twitter.
Froome finished second at the Spanish Vuelta two years ago and got a bronze medal in the Olympic time trial. He has shown good form this year by winning the Criterium International and Tour de Romandie.
Wiggins was looking to follow up his Tour success with a Giro win until his bid was derailed by illness.
Although his chest infection has cleared up, team doctor Richard Freeman says there are still concerns over his knee problem.
"However, further medical investigations on the knee injury that we were managing at the Giro showed the condition was more significant than we thought," Freeman said. "It has needed intensive treatment and, whilst it will be fully resolved, Bradley now needs to rest completely for five days before a gradual, return to full training over a period of two to three weeks."
Wiggins had to withdraw from the 2011 Tour early on after breaking his collarbone in a crash.
He has vowed to come back stronger from this latest setback.
"I've been through this before, when I broke my collarbone, so I know how it works. I'll get this sorted, set new goals for this season and focus on those," Wiggins said. "This team has so many riders in great shape, ready for selection and we set incredible standards for performance which shouldn't be compromised. We need to have the best chance to win."Suggest a correction