A special session of the UN's Human Rights Council was convened after the bloodiest day for Palestinians in years when 60 were killed on Monday by Israeli gunfire during demonstrations at the frontier fence.
"Nobody has been made safer by the horrific events of the past week," Zeid Ra'ad al-Hussein told the body. "[Gazans] are, in essence, caged in a toxic slum from birth to death; deprived of dignity; dehumanised by the Israeli authorities to such a point it appears officials do not even consider that these men and women have a right, as well as every reason, to protest."
The motion called for the urgent dispatch of "an independent, international commission of inquiry" but ran into opposition from the US and several European countries for being "unbalanced and over-politicised" in its wording.
However Prince Zeid said he supported the call for an investigation that is "impartial, in the hope the truth regarding these matters will lead to justice".
Israel says the deaths took place in protests organised by Hamas, the group that controls Gaza, that intentionally provoked the violence. Hamas claimed 50 of the protesters were its members but denied an attempt to storm the barrier using human shields.
The motion was carried with 29 votes in favour, two against and 14 abstentions.
Israel and the United States complained that the Human Rights Council, made up of 47 states chosen by the General Assembly, has an "automatic anti-Israel majority" because of the disproportionate number of countries hostile to Israel with U.N. seats.
Diplomats have separately proposed a security council resolution that would request UN Secretary-General Antonio Guterres to report within 30 days on "ways and means for ensuring the safety, protection and well-being of the Palestinian civilian population."
Israeli forces had killed 106 Palestinians, including 15 children, since March 30. More than 12,000 were injured, at least 3,500 by live ammunition.
The push for a resolution comes after the bloodiest day for Palestinians since the 2014 Gaza war.
Israel has said it is acting in self-defense to protect its borders and communities. Both Israel and the United States said Hamas, which rules Gaza, instigated the violence, an allegation denied by the militant group opposed to Israel's existence.
Danny Danon, Israel's UN Ambassador, has condemned calls for an inquiry as a "shameful" effort "to support Hamas' war crimes against Israel and the residents of Gaza who are being sent to die for the sake of preserving Hamas' rule."
During a Security Council meeting on Tuesday, US Ambassador to the United Nations Nikki Haley blamed Hamas for "inciting violence for years, long before the United States decided to move our embassy."
On Monday, the United States blocked a Kuwait-drafted council statement that would have expressed "outrage and sorrow at the killing of Palestinian civilians" and called for an independent and transparent investigation, diplomats said