Despite Froome being chosen as the team's 2013 official Tour leader, Wiggins announced this month that he wanted to go for a Giro d'Italia/Tour de France double.
Wiggins's comments prompted Froome to issue a statement saying he would be leading the team's challenge for the world's most famous cycling road race and not the Olympic time-trial champion.
But with Wiggins now ruled out, potential conflict between the two Sky riders will be avoided and Froome's victory hopes should be boosted.
"It's incredibly sad to have the reigning champion at Team Sky but not lining up at the Tour," Team Sky principal Dave Brailsford said in a statement. "But he's a champion, a formidable athlete and will come back winning as he has before."
In last year's race, Froome often cut a frustrated figure on the bike as he looked capable of beating his team leader.
The 28-year-old Froome has been in good form this year, winning the Tour of Oman, the Criterium International and the Tour of Romandie.
But he will still have plenty of challengers in the Tour de France, with former champion Alberto Contador among his main rivals.
Contador has won the race three times but was stripped of his 2010 victory after testing positive for an illegal substance.
He returned from a two-year ban to win the Tour of Spain last year and has said he deliberately did not enter the Giro d'Italia so he could concentrate on the Tour de France.
Brailsford told Sky Sports News he expected a different style of Tour this year.
"The opposition is very, very tough but we have great competitors, the team is ready and the guys are excited," he said.