In the face of bitter opposition from Baghdad, 65 out of 68 lawmakers present voted in favour of the September 25 poll as opposition members boycotted the parliament's first session in two years.
After the show of hands, lawmakers stood to sing the Kurdish anthem while others raised flags to the sound of applause.
The vote was to give a legal framework to the referendum that has also stirred protests from neighbouring states, especially Turkey.
The United States has proposed unspecified "alternatives" to which Barzani has pledged to give a rapid response.
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"If they have a stronger alternative to the referendum, the Kurdish leadership will look at it, but if they want (us) to postpone the vote with no alternatives, we won't," Barzani, who set the referendum date in June, said yesterday.
The session was the regional parliament's first in two years, and Barzani's mandate as president of the autonomous Kurdish region in northern Iraq officially expired in 2015.
Two opposition parties -- the independent Goran, which has 24 seats in the 111-seat parliament, and Jamaa Islamiya, which is close to Iran and holds six seats -- said they would boycott the session.
Today's session in Arbil followed two anti-referendum votes which passed earlier this week in the national parliament in Baghdad, both of which were boycotted by Kurdish legislators.
Turkey and Iran fear the referendum could stoke separatist aspirations among their own sizeable Kurdish minorities.
Ankara has warned of the "cost" to the Iraqi Kurds, whose economy is heavily dependent on oil exports via a pipeline running through Turkey to the Mediterranean.
Yesterday, the Baghdad parliament fired the governor of the northern province of Kirkuk, Najm Eddine Karim, over his provincial council's decision to take part in the non-binding Kurdish referendum.
Mixed regions such as Kirkuk are a highly sensitive issue in ethnically fragmented Iraq, with its Shiite-dominated government in Baghdad and large Sunni Arab and Kurdish communities.
In Kirkuk province, the different communities have been arming themselves while numerous paramilitary forces have taken up positions north and west of Baghdad as joint units advance against the retreating IS jihadists.
In the city of Kirkuk, Kurdish peshmerga fighters have taken charge of security, while Shiite paramilitary units have been deployed on the outskirts.
Iraqi Kurdistan, whose people were brutally repressed under Saddam Hussein, won autonomy in 2005 following the dictator's ouster in a US-led invasion under a constitution which set up a federal republic in Iraq.
The referendum would "not necessarily lead to (an) immediate declaration of statehood, but rather to know the will and opinion of the people of Kurdistan about their future", Barzani said in February.
Kurdish leaders have since reiterated that a "yes" vote would pave the way for the start of "serious negotiations" with the Baghdad government.