The Portuguese champions had been favourites coming into the clash, but their superior European experience counted for nothing as they were eliminated 2-1 on aggregate.
Pereira admitted once Defour was dismissed early in the second half, his side were up against it.
"Steven Defour's sending off influenced the match," he said.
"We tried to react even with ten men and control the game. Every event in the game made our life difficult."
The 44-year-old also pointed towards Joao Moutinho's injury at the end of the first half as another key moment that led to their exit.
"Joao Moutinho's injury also made life difficult. We had to make changes that we didn't expect," he said.