The council's resolution adopting the report was passed in Geneva by 25 votes to six with 11 countries abstaining and five declining to vote.
The United States and Israel were among those countries which voted against the resolution.
In addition to endorsing the report, the resolution "strongly condemns all policies and measures taken by Israel, the occupying power, including those limiting access of Palestinians to their properties and holy sites".
It also calls on Israel to stop digging and excavation work around the al-Aqsa mosque in occupied East Jerusalem as well as other Islamic and Christian religious sites.
Israel rejected the charges saying the resolution – drafted by the Palestinians with Egypt, Nigeria, Pakistan and Tunisia, on behalf of non-aligned, African, Islamic and Arab nations – threatened peace efforts.
The Goldstone report recommended that its conclusions be sent on to the International Criminal Court (ICC) prosecutor in The Hague if Israel and Hamas do not hold their own credible investigations into allegations of war crimes within six months.
The report accused Israel of war crimes and crimes against humanity.
It also accused the Hamas movement, which has de facto control of Gaza, of war crime violations, but reserved most of its criticism for Israel.About 1,400 Palestinians – the majority of them civilians - and 13 Israelis were killed during Israel's three-week war on Gaza, which had the stated aim of stopping rocket attacks by Palestinian fighters from the coastal territory.