During a thrilling contest at Education City Stadium, Ghana found themselves 3-2 up after Mohammed Kudus' second goal of the game halted South Korea's momentum.
The Taeguk Warriors, who had previously fought back from 2-0 down thanks to a Cho Gue-sung brace, piled the pressure on at the end and got themselves a corner.
But referee Anthony Taylor blew for full-time before they could take the set-piece, sparking a frustrated reaction from Bento, whose side were left bottom of Group H with one point heading into their final game.
Bento's red card meant he was banned from taking part in the post-match media conference, but his assistant Sergio Costa was more than willing to state his boss' case.
"Totally unfair," Costa said of the situation. "In the first half they let a similar situation be played.
"The referee took that opportunity away, Paulo reacted. He said nothing that was inappropriate to the referee, but he does what he knows. I think it's a lack of fairness.
"I think the reaction is one of a person and group who feel lack of fairness at the end of the match.
"[Bento] is emotional and defends his own until the last. We are all able to understand his reaction.
"That sometimes leads to reactions that are part of what a human being is made of. It was normal of someone who did everything for the win.
"I believe we should feel sad, feel a lack of justice at the end, but also be proud. We gave our souls and that's something we'll try to repeat."
While Bento's absence for South Korea's crucial final group match – which they need to win – against Portugal is far from ideal, Costa suggested the situation will boost the team's unity.
"We shall continue to prepare in same way as other matches - our strategy will not fail," Costa added. "He won't be present on the matchday, which is a loss because Paulo is obviously a great manager, but I think it will bring us together."
Kudus proved decisive for Ghana after also impressing against Portugal on matchday one, with his brace on Monday making him the second-youngest African player ever to score twice in a World Cup game.
Ghana coach Otto Addo seemed reluctant to lavish Kudus with praise before the game, but he was more forthcoming afterwards and reserved a special mention for the Right To Dream academy, where the Ajax midfielder honed his skills as a youngster before making the most of their link-up with Denmark's Nordsjaelland.
Addo said: "He's a good character, like everyone else. He's a good player who is good one-on-one; he's fast and has very good game intelligence.
"He has to work more defensively, for sure, but he's on the right track to be a great player. I just have high praise for him.
"I've known him for six or seven years, from the time I was working as an assistant at Nordsjaelland, where we have a cooperation with the Right to Dream academy, so also congratulations to them, for this really, really good education.
"Players like him and Kamaldeen [Sulemana] are extraordinary on and off the pitch. They are good guys, good characters. Congratulations to [Right to Dream] for creating such a player."