Pogacar, who won his third Tour on Sunday, was not selected because of fatigue, the committee said in a statement.
Pogacar was one of the favourites, alongside Dutchman Mathieu van der Poel, for the Olympic road race on August 3.
"The national coach of the men's cycling team revealed the names of the riders who will compete in this year's Olympic Games in Paris. Tadej Pogacar, ... being too tired, will not be among them," the Slovenian Olympic Committee said.
"He will be replaced by his national team colleague Domen Novak.
"We congratulate the winner of the race across France for another victory in the most prestigious cycling race in the world, and we hope that he will represent the colours of Slovenia at the upcoming Summer Olympics in Los Angeles in 2028."
Pogacar's ability to perform on one-day races with steep hills made him a top contender in the Paris road race, a gruelling 225km course in and around the French capital.
Pogacar has won the Tour of Flanders, the Giro di Lombardia and Liege-Bastogne-Liege, three of the one-day classic races.
Triple crown
Meanwhile, Pogacar wants to put his name on an elite list by targeting the "Triple Crown" of cycling.
Pogacar is the first man to win the Giro and the Tour in the same season since Marco Pantani in 1998, and only the eighth rider ever to do so, and he did it emphatically, winning the final three stages and making it six stage wins overall.
No rider has ever won all three Grand Tours in one year, and Pogacar has no intention of tackling Vuelta a Espana this year, something he had previously said during the Giro and which he reiterated after his success in France.
"For sure it crossed my mind to do the Vuelta, people tell you to go do this or that, so of course it was there," Pogacar said. "But I'm trying to let it go in one ear and out the other."
Instead, Pogacar is aiming for the Triple Crown of cycling - adding the world road race championship, where he finished third last year as Mathieu van der Poel took gold, to his two grand tours.
That triple has only been achieved twice in men's cycling, by Belgium's Eddy Merckx in 1974 and Irishman Stephen Roche in 1987, and Pogacar has now given himself more time to recover as he will no longer compete in the Paris Olympics.
"For me, putting a cherry on top of this season would be to have a really nice August, to relax a bit, to prepare well for the World Championships and then give it my all there," Pogacar said.
"Next I want to take the world championship jersey. I know that Mathieu looks good in the rainbow jersey, but I want to take it from him."
Cavendish call
British cyclist Mark Cavendish has confirmed that he has taken part in his last Tour de France, having finally broken the all-time record for most stage wins at the Tour.
Cavendish had been level on 34 stage wins with Eddy Merckx since 2021 but this year he sprinted to victory on stage five to make the record his own, and now the 39-year-old can bow out in style.
"I think now it's time. I've done 15 Tours de France and I've created some incredible memories of the Tour de France," Cavendish told Reuters.
"This race has given me a life I could only dream of. It's given me the highest of highs and the lowest of lows."
Cavendish had announced his retirement last year but changed his mind in an attempt to go out the way he wanted having crashed at last year's Tour.
- Reuters