The decision to hand Germany a penalty following Joao Pereira's challenge on Mario Gotze and Pepe's dismissal for clashing with Thomas Muller frustrated Bento, who believes that the Serbian official had a big say on the outcome of the match.
"These were the two things that seemed to show bias and they were both decisive," the 44-year-old told members of the media.
"The penalty was forced and I don't know if [Pepe] was sent off because of his reputation.
"I'm not saying it was the referee's fault only. We did make mistakes, not only in our defence but also in the sharpness of our attack."
Portugal return to action against the USA on Sunday night.