The Seleccao finished as runners-up in Group F, despite strolling to a 3-0 win in the last fixture against Luxembourg on Tuesday while Fabio Capello's men drew against neighbours Azerbaijan.
Bento's men were left to rue draws against Israel as they trailed Russia by a single point with all games played, but the 44-year-old head coach was realistic about his side's final position and insisted the team would give their all in the play-offs.
"We weren't the best team in this group," Bento told reporters. "The best were [Russia] who came first.
"We should have stayed in first. The value of the team and these players is not the issue.
"Now we have more things to think about, that mean we cannot prepare in the best way to be at the 2014 World Cup.
"Portugal will do everything to go to Brazil."
The European play-off draw for a place in Brazil next summer will be on Monday, with Cristiano Ronaldo and Co. likely to face either France, Romania, Ukraine or Iceland.