Although Aguirre has denied any wrongdoing and vowed to clear his name, the Japan Football Association fired him on Tuesday fearing the ongoing scandal could affect the team's bid to qualify for the next World Cup.
"It was brief, but he trusted us and we fought together," Japan captain Makoto Hasebe was quoted as saying by Kyodo news agency of the Mexican's 10-game stint with the side.
"I hope things turn for the better for him from here on," said the 31-year-old Eintracht Frankfurt defensive midfielder.
Aguirre, a former Mexico and Atletico Madrid manager, was appointed as head coach after Alberto Zaccheroni was dumped when Japan failed to make it past the first round at last year's World Cup in Brazil.
The 56-year-old Aguirre oversaw Japan's unsuccessful Asian Cup title defence in Australia where United Arab Emirates stunned them in the quarter-final but was still popular among the players.
"What I remember about him most is that he used to have a good time at the training sessions," said defender Atsuto Uchida.
"Since I've been playing for Japan, I don't know of any other coach who had as much fun at training and he used to run the sessions well.
"The manager must be hurting the most. But I understand where the JFA is coming from as well."
Full-back Yuto Nagatomo was personally grateful to the man who showed faith in him.
"I'm very disappointed by the dismissal. We did everything we possibly could at the Asian Cup. He kept picking me and made me feel important to the team," the Inter Milan full-back said.
"I want to thank him for all that he did for us."
(Reporting by Amlan Chakraborty in New Delhi; editing by Sudipto Ganguly)
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