The Dragoes coach claimed his side were undermined by refereeing and an injury after the Portuguese champions slipped out of the Champions League 2-1 on aggregate to Malaga
The Porto coach felt aggrieved by the decision to red card Steven Defour and felt the officials were more lenient towards the hosts.
"We knew we were going to find Malaga to be an aggressive team but our aggression was punished with yellows and theirs was not," Pereira said.
Isco's well-taken goal levelled the tie at the break and the hosts dominated the second half after Steven Defour was shown a red card in the 49th minute.
Paraguay striker Roque Santa Cruz came off the bench to secure the win with a header 13 minutes from time.
Pereira argued the sending off coupled with an injury to talisman Joao Moutinho proved the difference between the two sides on the night.
"Defour's sending-off and Moutinho's injury influenced the match," he continued.
"Moutinho started to feel uncomfortable and they scored right at the end of the first half. Then the second half started with the red card and the game became more difficult.
"We tried to react, even with 10 men, to control the game. Every event in the game made our life difficult.
"We are sorry to exit the race. I think the fans are sad, but there is no one sadder than the players."