Mancini, one of the highest-profile foreign coaches to join the Russian Premier League in recent years, signed a three-year contract with Zenit in 2017.
However, the club said the contract, which will come to an end on Monday, had been severed through mutual consent and without any compensation payable.
Zenit and Roberto Mancini have reached an agreement to mutually part ways. Today's game will be his last match at Zenit
— FC Zenit in English (@fczenit_en) May 13, 2018
This month, Italian football federation commissioner Roberto Fabbricini said Mancini had held talks with Italian football officials but that no deal had been reached.
Zenit, bankrolled by Russian energy giant Gazprom, have used their deep pockets to attract foreign managers in the past, including Dick Advocaat, Luciano Spalletti and Andre Villas-Boas.
Mancini, who has coached a number of elite sides including Inter Milan, Galatasaray and Manchester City, led the latter to a first English title in 44 years in 2012. Zenit are currently fifth in the Russian Premier League with one game remaining.
Italy have a managerial vacancy after Gian Piero Ventura was sacked when the four-times champions failed to qualify for this year’s World Cup finals taking place in Russia from June 14 to July 15.