The midfielder picked up two yellow cards at La Rosaleda as a 2-0 loss on the night saw Porto exit the competition 2-1 on aggregate.
"Steven Defour's sending-off influenced the match," Pereira told reporters.
"We tried to react even with 10 men and control the game. Every event in the game made our life difficult."
Isco and Roque Santa Cruz scored the goals for the hosts, who are taking part in the Champions League for the first time this season.