Malafeev eventually became the first-choice goalkeeper ahead of Kamil Čontofalský and won the UEFA Cup in 2008 after keeping a clean sheet against Rangers in the final.

After a long-term injury in May 2005, Malafeev lost his place in the goal for Zenit and Russia to Kamil Čontofalský and Igor Akinfeev, respectively.

In 2007, played in two Euro 2008 qualifiers against Andorra and Croatia after Akinfeev's long-term injury but was relegated to the bench in favor of Vladimir Gabulov.

After Zenit's successful UEFA Cup campaign he lost a narrow battle with Igor Akinfeev for the first choice goalkeeper spot in Russia's Euro 2008 squad.

[2] After the UEFA Euro 2012 he announced that he is retiring from the national team to spend more time with his children, but is prepared to be called up in case of emergency such as injuries to other top goalkeepers.