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Korea Republic pulled off a late 2-1 win over Portugal in its final group game to reach the last 16, where it was beaten 4-1 by Brazil.
Bento, appointed in 2018 as Shin Tae-yong's successor, announced immediately after that match he would not be renewing his contract with Korea Reublic.
The Portuguese coach said a final farewell to supporters on Wednesday (AEDT) before flying back to his homeland.
"I am thankful to all the players, due to their professionalism, work ethic and their behaviour," Bento said. "They gave me the opportunity to have one of the most beautiful experiences of my life, which I will never forget.
"Personally I have no words to thank you all for the respect, affection and support you showed during this amazing experience."
Korea Republic also drew 0-0 with Uruguay and lost 3-2 to Ghana in Group H, with its win over Portugal enough to see it through on goals scored.
It was the first time since 2010 that the Asian nation had made it past the first hurdle, though it was outclassed by Brazil in a one-sided last-16 tie.
The Taegeuk Warriors intend to name Bento's successor by February ahead of the next international break.