Ronaldo stormed off the pitch at the final whistle and subsequently pulled out of the team's training session on Monday.
However, Bento has dismissed claims that both incidents stemmed from an argument, but did apologise to the Portuguese supporters for his captain's behaviour in Lviv.
"Players react to different situations in different ways. If anyone was offended, I'd like to apologise, because I'm responsible," Bento told reporters.The 42-year-old also responded to criticism from former international team-mates Luis Figo and Rui Costa, who lamented his defensive approach against the Germans.
"Everybody is talking about the strategy with the national squad," he continued.
"I won't say anything against Luis or Rui, they're my colleagues. But they know it's harder to do something than say something.
"We created more chances than Germany did but the only thing that will be remembered by history is that we lost to Germany 1-0.
"We wanted to play on the counter-attack against the French in 2000 and we lost the game. We [also] lost the first game in 2004 and still got to the finals."
Portugal will be eliminated if they lose to Denmark on Wednesday.