In a resolution adopted by consensus, the council mandated UN rights chief Zeid Ra'ad Al Hussein to send a group of "eminent experts" to Yemen, where a Saudi-led coalition had been bombing Huthi rebels since March 2015.
The group will then "carry out a comprehensive examination of all alleged violations and abuses of international human rights" committed in the conflict and try "to identify those responsible."
Launching the probe marks a victory for a group of European states and Canada which pushed hard for an international inquiry fully independent of the Yemeni national investigation, which the Saudis support.
The Iran-backed Huthi rebels have also been accused of major violations, which the UN team will also probe.
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Saudi Arabia had for the past two years succeeded in blocking the rights chief's call for an international investigation.
In a letter leaked to several media outlets this week, the kingdom threated economic and diplomatic retaliation against rights council members which voted for the EU/Canadian proposal.
The Saudi envoy to the council, Abdulaziz Alwasil, ended up endorsing today's resolution, which was slightly softer than previously EU proposals.
Countries with significant and lucrative ties to Saudi Arabia, including the United States, Britain and France, were reported to be seeking a compromise between the EU and Arab camps, which were deadlocked through the week on a resolution.
The war in Yemen has killed more than 8,500 people and wounded nearly 49,000 others, according to the World Health Organization.
More than 17 million Yemenis are now facing dire food shortages, and a nationwide cholera epidemic has killed more than 2,100 people since April.
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