FIFA confirmed the punishments amid reports that the Portuguese Football Federation had appealed Pepe's sending off, but both he and Pereira are suspended for the next match.
Pepe was given his marching orders after headbutting Thomas Muller following a tangle in his side's 4-0 defeat to Germany on Monday.
Paulo Bento claimed referee Milorad Mazic "showed bias" in awarding a penalty as well as a red card, but the Portugal coach will now be without the defender for their second Group G clash with the United States on Sunday.
Pereira will also miss his side's next game, which comes on Thursday against England in Group D.
The Benfica full-back was dismissed for kicking out at Joel Campbell late in the 3-1 defeat to Costa Rica on Saturday.
Uruguay's clash with England will prove crucial in determining who progresses through the group after both teams lost their opening games.
