It said Yitzhak Yossef was elected Sephardi chief rabbi and David Lau the Ashkenazi chief rabbi.
The responsibilities of the chief rabbis include the country's rabbinical courts and regulating the food supervision industry.
Today's election, held in a Jerusalem hotel, involved a 150-strong electoral college of religious and secular officials including mayors of the main cities.
Yossef is the son of Ovadia Yossef, founder and spiritual leader of the opposition ultra-orthodox Shas party, which has 12 seats in parliament.
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For the first time, 10 women were members of the electoral college, despite women not being represented in rabbinical courts or in the grand rabbinate.
The institutions over which the grand rabbis preside have a major bearing on the lives of Israeli Jews in a country where the separation of church and state does not exist.
Jews cannot marry or divorce without rabbinical approval, and those seeking to marry must present proof of their Jewish heritage before rabbinical courts.
This stipulation has meant that many thousands of secular Jews or those unable to prove their Jewishness have gone abroad to be married in civil ceremonies instead.