The Czech skipper has failed to fully recover from an injury picked up in the group stages and misses out on the starting XI for the second consecutive game
The Arsenal midfielder only resumed training on Wednesday from an achilles tendon injury picked up in his side's group match against Greece on June 12, which also forced him to sit out the victory over Poland four days later.
However, his recovery has not been enough to convince coach Michal Bilek of a place in the starting XI, and the skipper will now begin the game on the bench.
Vladimir Darida starts in place of David Kolar in midfield to mark the only change for either side heading into today's match. The Viktoria Plzen youngster, who was a late call-up to the Czech's Euro 2012 squad to replace the injured Daniel Pudil, will make his first appearance of the tournament.
Meanwhile, Portugal coach Paulo Bento has named an unchanged lineup from his side's 2-1 victory over Netherlands on June 17.
Helder Postiga continues to lead the line for the Seleccao ahead of Silvestre Varela and Nelson Oliveira.
Two-goal hero Cristiano Ronaldo continues on the flank for Portugal alongside Manchester United winger Nani, as Bento looks to build on his side's promising attacking display against the Netherlands.
Czech Republic (4-5-1): Cech; Selassie, Kadlec, Sivok, Limbersky; Hubschman, Plasil, Jiracek, Darida, Pilar; Baros
Portugal (4-3-3): Patricio; Pereira, Alves, Pepe, Coentrao; Veloso, Moutinho, Meireles; Nani, Ronaldo, Postiga.