Delegates at the US Episcopal Church conference rejected a motion only two days after electing a female leader in a move that has already caused comments of concern from the world body.
Most of the branches of the Anglican Communion around the world have resisted elevating women to bishops and oppose homosexuality.
Many severed or restricted ties to the US church after it named an openly gay bishop in 2003.
International church leaders warned before Tuesday's vote that the Anglican communion could break apart if the US church does not impose a moratorium until Anglicans worldwide reach a consensus on the issue.
But the Episcopal convention in Columbus, Ohio stumbled over the more simple response of issuing an apology for the controversy.
Delegates spent all day on Monday in discussions that watered down a resolution to apologise for "straining the bonds of affection" from "breaching the proper constraints."
A majority of delegates on Tuesday then rejected the more contentious resolution to "refrain from" nominating gay bishops or developing rites for the blessing of same-sex unions.
Female appointment
The election of Bishop Katharine Jefferts Schori as the Episcopal Church's leader at the general convention on Sunday was seen by some observers as a potential provocation of the dispute.
Pittsburgh Bishop Robert Duncan, a leading voice of the conservative wing of the church, said Ms Jefferts Schori faces "an impossible task."
"For the Anglican communion worldwide, this election reveals the continuing insensitivity and disregard of the Episcopal Church for the present dynamics of our global fellowship," Mr Duncan said in a statement.
The election will be particularly difficult for the three US dioceses that do not ordain women, Mr Duncan added.
Ms Jefferts Schori is part of the church's liberal majority and backed the ordination of openly gay bishop Gene Robinson in 2003. She also supports church blessings of same-sex unions.
She worked hard to bring about reconciliation with church members who opposed his ordination, said Reverend Barbara Lewis, who serves as Ms Jefferts Schori's secretary.
Bible's interpretation not literal
On Monday, Ms Jefferts Schori said that homosexuality is not a sin and that the Bible should not be interpreted literally.
"The Bible has a great deal to teach us about what it means to live as a human being. The Bible does not have so much to teach us about what sorts of food to eat, what sorts of clothes to wear," she told CNN.
"The Bible tells us how to treat other human beings and that is certainly the great message of Jesus to include the unincluded."
The Archbishop of Canterbury, Rowan Williams, who has been working to prevent a rift, issued a lukewarm welcome to Ms Jefferts Schori Monday, sending "good wishes as she takes up a deeply demanding position at a critical time."
Dr Williams, the religious head of the church, warned that the whole Anglican church was now facing "exceptionally difficult choices."
"Her election will undoubtedly have an impact on the collegial life of the Anglican Primates; and it also brings into focus some continuing issues in several of our ecumenical dialogues," Dr Williams said in a statement.