Endo suffered a serious left foot injury earlier this year and underwent surgery in February, his recovery limiting him to a single Premier League start for Liverpool all season, in a 1-0 win away at Sunderland.
The 33-year-old had targeted a return in time for the tournament, co-hosted across the United States, Canada and Mexico, and made his comeback in a 1-0 warm-up win over Iceland on May 31, coming off at half-time. He travelled with the Japan squad to the United States and continued physical therapy, but the injury proved too significant to overcome.
Earlier this week, Endo posted an emotional message on social media confirming he would not be able to play at the World Cup and announcing his retirement from international football, ending a decade-long international career.
The decision left Ajax defender Ko Itakura to take over the captaincy for Japan's opening match against the Netherlands on Sunday, with Borussia Monchengladbach forward Shuto Machino added to the squad as Endo's replacement.
Speaking to media, Moriyasu explained the process that led to the call, describing it as one based on consistent medical feedback throughout Japan's preparations.
"As the head coach, I was the one who made the final decision. I'd been receiving reports from the medical staff. During the game with Iceland, he was not able to perform on the pitch for a long time."
The Japan coach said the team had given Endo every chance to prove his fitness before reaching a conclusion.
"We had him try as best as he could and also had the medical staff looking after him."
Ultimately, concerns over Endo's ability to sustain performance levels across a demanding tournament schedule tipped the balance.
"We discussed that throughout the World Cup, it may be difficult for him to perform for the entire period of the games, therefore I made the final decision looking at his condition."
Moriyasu acknowledged the emotional weight of delivering the news to a player who has been central to the squad's identity since the 2022 World Cup in Qatar.
"It felt really bad for me to give him such a message. Of course, it's impossible to know exactly how he felt or know what his thoughts were, but he was very understanding and respectful and we could maintain our good conversation in a cool manner."
Endo leaves the national team with 73 caps and four goals, having represented Japan at the 2018 and 2022 World Cups and led the side through a period in which beating major footballing nations became less of a surprise and more of an expectation.
For Moriyasu's squad, the timing could hardly be tougher, losing their captain and on-field leader just three days before facing one of the tournament's heavyweights. How Japan respond to the upheaval, on top of the long-standing absence of injured winger Kaoru Mitoma, will say much about the depth Moriyasu has built into this group heading into the knockout stages.