Russia, which is undefeated in seven games and bidding for its first title since 1993, will next play either the United States or Finland. The Czechs, who have four of the last eight titles, had reached the final at the last two championships, winning gold in 2005.
Andrei Markov gave Russia the lead in the first period and Malkin scored two of Russia's three goals in the final period. Alexander Eremenko made 27 saves to earn the shutout.
Alexander Frolov sent a backhand pass across the slot to Markov, who fired it over Roman Cechmanek's right shoulder on the power play 6:48 into the opening period.
After a scoreless second period, Ilya Kovalchuk sent a slapshot from the circle that bounced off the end boards and onto Malkin's stick. The Pittsburgh Penguins forward put the rebound through an opening between Cechmanek's right foot and the post to make it 2-0 only 23 seconds into the final period.
Cechmanek later came out of his crease in a risky move and fell. Alexander Radulov took advantage of the scramble by sending a slapshot past the goalie, who had dropped his stick.
Malkin added the fourth goal on a breakaway. With Czech Republic defenceman Zbynek Michalek chasing, Malkin scored a wraparound goal with five minutes to go.
Russia has scored a tournament-leading 39 goals this year.
No host country has won the worlds since 1986, when the Soviet Union was undefeated in 10 games.