The Czech team scored in overtime to secure a place in the semis.
Unbeaten in the six games of the tournament, Russia had topped qualifying group Group F to take on the Czechs, who finished in fourth place in Group E, losing to the U.S. in its last qualifying match.
Washington Capitals forward Alexander Ovechkin netted in the third minute to give Russia an early lead with an assist from Yevgeny Malkin.
Russia missed at least four chances to double the lead, fell back when Chezh player Tomas Kaberle scored in the second period, and Jaroslav Hlinka early in the third.
Sergei Mozyakin gave Russia an equalizer, but Patrik Stefan put the Czechs ahead with a short-range goal within a minute. The Czech squad seemed to have secured their place in the semis, until Aleksei Mikhnov scored with just one minute to go, sending the game into overtime.
Late in overtime Czech forward Zbynek Irgl seized the puck near the Russian goalmouth, to strike over goaltender Maxim Sokolov who was flat on the ice.
Russia had beaten the Czech Republic in all the four games in the 2005/2006 Euro Hockey Tour to win the competition, which is considered to be the unofficial European Championship.
