"Dick Advocaat has chosen St. Petersburg and Russia," Sergei Fursenko said.
Advocaat had earlier agreed to take command of the Australian national team. However, he changed his mind after taking Zenit to their first league title since 1984 earlier this month, subsequently earning the team a Champions League place for 2008/09.
Russian gas giant Gazprom bought a controlling stake in Zenit in 2005, and immediately set about buying up top players, both Russian and foreign, leading many Russians to dub the side "the Russian Chelsea."
Dick Advocaat's salary is believed to be over $4 million a year, which would make him the highest-paid manager in Russia.
Zenit may now be forced to pay compensation to the Australian FA.
The Dutchman began work with Zenit in June 2006 after a spell as South Korea manager. He also took his native Netherlands to the last eight of the 1994 World Cup and the semi-finals of Euro 2004. His career has also seen title triumphs with PSV Eindhoven and Glasgow Rangers.