Portugal coach,, Paulo Bento, said the 'biased' referee was the reason his side were thumped 4-0 by Germany in their opening Group G, 2014 FIFA World Cup match on Monday.
Pepe was shown a straight red card after head-butting Thomas Muller in retaliation for the German striker play-acting after a collision with the Portuguese defender.
At the time Portugal were trailing 2-0 after a Muller penalty and a Mat Hummels header.
Bento admits they were in control of the match until the opening goal, but insists the sending off of his defender turned the game in favour of the Germans.
“The first half was the problem for us,” said Bento.
“With the exception of the first few minutes, when we made a slow start, we were pretty much in control of things, and it was a fairly even game until the first goal.
“In the second half we just tried to cope with being a man down the best we could. It’s very strange to have someone sent off in a game like this. That’s pretty much what the match hinged on.”
Bento claimed that the referee played his part with two biased decision, which decided the game.
"These were two things that seemed to show bias and they were both decisive," he added.
"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."