Endo, who endured an injury-hit season with Liverpool, has been replaced by Borussia Monchengladbach striker Shuto Machino, the Japan Football Association said in a statement.
"Since my injury, I've done everything I possibly could up to this point, so I have no regrets whatsoever," Endo said in a social media post.
The 33-year-old said he was frustrated at not being able to participate in the showpiece event but took pride in the team's growth since the 2022 World Cup in Qatar.
"With this campaign, I will be retiring from the national team. So from here on, I'll be cheering for the Japan national team as one of the fans," he said.
Japan are in Group F and kick off their eighth appearance at the World Cup finals against the Netherlands in Dallas on June 14th before taking on Tunisia and Sweden.