The 33-year-old midfielder had been expected to lead Japan as captain at the tournament after working his way back from a foot injury suffered while playing for Liverpool in February.
He was initially included in the squad, but Japan confirmed on Thursday that he would not take part after failing to recover in time.
Endo spoke openly about his disappointment, but said he had no regrets about his efforts to return.
"Since my injury, I've done everything I possibly could up to this point, so I have no regrets whatsoever," Endo said.
Despite his withdrawal, Endo used the moment to confirm the end of his international career with Japan, closing a chapter that saw him become a key figure in midfield and a respected leader within the squad.
He made 73 appearances for Japan, scoring four goals, and became known for his discipline, leadership, and consistency in midfield.
"From here on, I'll be cheering for the Japan national team as one of the fans," he added.
Japan will now head into the World Cup without one of their most experienced players, with group-stage matches against the Netherlands, Sweden, and Tunisia awaiting them in Group F.
Canada's wait for a first FIFA World Cup point finally ended on home soil as Cyle Larin's late strike rescued a 1-1 draw against Bosnia and Herzegovina in the nations' Group B opener in Toronto.
Former Orlando Pirates and Bafana Bafana coach Augusto Palacios has urged South Africans not to pin blame on Sphephelo Sithole following the 2-0 loss to Mexico.
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We take a look at South Africa's disappointing 2-0 loss to co-hosts Mexico in the opening clash of the FIFA World Cup 2026 in North America.
