The four-time champions and pre-tournament favorites were beaten 2-1 by Iran on Saturday in the quarter-finals, having thrown away a first-half lead.
Iran won it with a stoppage-time penalty but in truth they were comfortably the better team in the second half and had several big chances to bury the game before that.
Coach Hajime Moriyasu's job seems safe but it capped a torrid campaign for Japan, who were never really convincing in their three wins and two defeats in Qatar.
They had problems off the pitch too, with winger Junya Ito leaving the squad after an allegation of sexual assault and goalkeeper Zion Suzuki racially abused online following a string of mistakes.
Ito strongly denies the accusation, which relates to an alleged incident in Osaka last year.
Former Japan star Keisuke Honda, who was part of the team that won the Asian Cup in 2011, said the country's football needed "innovative change".
"The strides we have made until now have been thanks to the football association but it can't go on like this," he wrote on X, formerly known as Twitter.
Japan were not helped against Iran by a disastrous performance by center-back Kou Itakura, normally one of their most reliable players.
The Borussia Monchengladbach defender was caught flat-footed for Iran's first goal and got himself into a horrible tangle to give away the decisive penalty.
Itakura was inconsolable after the game, disappearing straight down the tunnel and later blaming himself for the defeat.
"After giving a performance like that I'm not qualified to go out onto the pitch as a national team player," he said.
Itakura was booked midway through the first half but Moriyasu kept him on the pitch for the whole game.
The coach later said he had misplayed his substitutions, and was powerless to stop Iran overwhelming his side with a second-half display of strength and aggression.
"Most of our players play in Europe so we're used to that kind of power, but in the second half we were completely dominated," said forward Ritsu Doan.
Wake-up call?
Japan arrived in Qatar on a run of nine straight wins where they scored 39 goals.
They began their tournament with a 4-2 win over Vietnam but had been behind for a while and looked shaky at the back, especially with the inexperienced Suzuki making a mistake for one of the goals.
In their next match they went down in a deserved 2-1 defeat to Iraq, before beating Indonesia to seal their place in the knockout rounds.
They looked more like the real deal in beating Bahrain 3-1 in the last 16, although they again failed to keep a clean sheet, and their preparations for Iran were thrown into turmoil by the Ito situation.
After some public flip-flopping from the Japan Football Association, Ito left the squad, with JFA president Kozo Tashima saying they wanted to protect the team from "noise".
Tashima later said there was no connection between Ito's departure and the defeat to Iran.
"The players are all professionals and whatever happens they are at a level where they are able to respond to it," he said.
Tashima also said he was "not thinking at all" about replacing Moriyasu, who has been in the job since 2018.
The coach led Japan to the last 16 of the 2022 World Cup after beating both Germany and Spain, and he has won two games out of two so far in qualifying for 2026.
Japan return to World Cup qualifying with back-to-back games in March against North Korea, home and then away in Pyongyang.
Writing in Nikkan Sports, columnist Sergio Echigo said Japan's Asian Cup exit must serve as a wake-up call.
"It's all been a sweet dream until now, winning 10 games in a row and beating big teams in Europe," he wrote.
"Our eyes have been turned towards the rest of the world. Have we woken up from the dream yet?"