The Frenchman is stepping down after his four-year spell in charge of the co-hosts, following their exit at the second round stage.
It was a great achievement, although I think we could have gone further
"Our great adventure is over," said a tearful Troussier.
"Today I was very proud to be their trainer and to have worn the Japanese shirt for four years.
"I say bravo to this Japanese team. I would tell the Japanese players to believe in their potential and their capacity to succeed."
Troussier's team reached the last 16 for the first time in their history after recording their first win in the World Cup.
"They have proved they can take on the top teams in the world and there is some recognition in European football now of our players," he said.
Troussier hopes the Japan side will carry on the development they have shown in the finals, where they were surprise winners of Group H.
"We showed a great dynamic for the future and I hope this Japanese team pushes on and the federation keeps the same rhythm of preparation," he added.
Star midfielder Hidetoshi Nakata also hailed the team's performance in the first World Cup to be held in Asia.
But the Parma playmaker feels they could have done even better.
"It was a great achievement that we made it to the last 16 although I think we could have gone further," he said.
"I am very disappointed with this defeat because we played well. I hope that the world is going to look at Japan differently from now on.
"It was a very tough match but we fought hard.
"I now wish all the best of luck to South Korea."