The measure still must be ratified by scores of ministers and elders nationwide before it can become part of the Book of Order, the constitution for the 2.6 million-member denomination.
It passed the church's General Assembly by a vote of 268-251, with four abstentions. If the ministers and elders in the church's 173 presbyteries approve, the ban would be put into effect at next year's meeting of the General Assembly.
A similar ban on gay commitment ceremonies was approved by the church's General Assembly in 1994 but failed to win ratification.
After the vote, gay-rights advocates streamed out of the meeting, many of them in tears.
"We are crying out for justice and we are crying out for this church," the Rev. Jane Adams-Spahr of San Rafael said as she led in prayer a group of some 50 opponents of the ban.
Several said they were still hopeful that the church's presbyteries would not uphold the ban.
No state has officially legalized gay marriage, but a new Vermont law legalizing civil unions for same-sex couples took effect Saturday, and other states have debated similar laws.
A month ago, the church's highest court ruled that local congregations may conduct such religious ceremonies celebrating homosexual unions as long as those ceremonies stop short of marriage.
But the amendment approved Friday night, if ratified, would overpower that ruling by prohibiting church officers from performing gay commitment ceremonies and barring such ceremonies from church property.
The Presbyterian Church (U.S.A.) prohibits homosexuals from serving as ministers but does not exclude homosexuals from the church.
Proponents of the ban argued that the Presbyterian Church must stop blessing same-sex unions because that implicitly condones homosexual behavior, which the church views as a sin.
Other supporters said recognizing gay couples could cripple the church's missionary work in countries with conservative values.
The Rev. Charles Castles of San Joaquin, whose presbytery proposed the amendment, said he considered Friday's vote a "step of the journey" toward clarifying the church's stance on homosexuality.