The Liverpool midfielder pulled out after failing to recover from a foot injury, and was replaced by Borussia Monchengladbach’s Shuto Machino.
The 33-year-old Endo said on social media that he was “frustrated” at not being able to play but backed his team to impress in Group F, where they face the Dutch, Tunisia and Sweden.
“There will definitely come a time in the future when Japan win the World Cup, so let’s believe in that and support the team,” he wrote on X.
“Let’s bring the strength of Japan together so that that moment can happen at this tournament in North America.”
He added: “I have decided to retire from the national team. From now on, I will be supporting Japan as just another fan.”
Endo suffered a season-ending foot injury playing for Liverpool against Sunderland in February but returned for Japan in a 1-0 friendly win over Iceland in Tokyo on May 31.
He came off at half-time, continued to feel discomfort and was not involved in any full training sessions.
He took part in training when Japan moved to their World Cup base in Nashville on Monday but was unable to recover in time.
“I’ve done everything in my power since I sustained the injury so I have no regrets,” said Endo. “Of course I’m frustrated that I can’t play at this World Cup.
“But more than that, I’m proud that I’ve been able to captain this team since the Qatar World Cup and help it grow into a group where it feels natural to say our target is to win the World Cup.”
Endo made his Japan debut in 2015 and retires with 73 caps, having scored four goals for his country.
He was a member of Japan’s squads for the 2018 and 2022 World Cups, and played in their stunning wins over Germany and Spain in Qatar.
Defender Ko Itakura will take over as Japan’s captain at the World Cup.
Japan have been hit hard by injuries.
Brighton winger Kaoru Mitoma was left out after injuring his hamstring less than a week before coach Hajime Moriyasu named his squad.
Monaco’s Takumi Minamino also missed out after tearing the anterior cruciate ligament in his left knee in December. (AFP)