Pogacar, who won his third Tour on Sunday, was not selected because of fatigue, the Slovenian Olympic Committee said in a statement.
Pogacar was one of the favourites, alongside Dutchman Mathieu van der Poel, for the Olympic road race on August 3rd.
"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 on Sunday became the first rider to achieve the Giro d'Italia/Tour de France double since 1998.
His ability to perform on one-day races with steep hills, however, also 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, Il Lombardia and Liege-Bastogne-Liege, three of the one-day classic races.
Many riders tend to peak around the end of the Tour and ride their wave of form into the Olympics.
Defending champion Richard Carapaz, who won the mountains classification at this year's Tour de France, was not selected by Ecuador.
