Porto held a 1-0 win from the first leg but were defeated 2-0 on the night, but Pereira felt that his team would have won had circumstances been different.
"Defour's sending-off and Moutinho's injury influenced the match," UEFA.com quotes Pereira as saying. "Malaga played very aggressively, especially from the middle of the first half, in front of their supporters, and the yellow cards we collected hindered our football.
"Moutinho started to feel uncomfortable and they scored right at the end of the first half. Then the second started with the red card for Defour and the game became more difficult."
Pereira has been in charge of Porto since 2011.