The Methodist General Conference voted 428-405 to delay all discussion of church policy related to LGBT people during a meeting in Portland, Oregon. Critics see the group as more anti-Israel than pro-peace.
The petition described the group a "one-sided political coalition", citing its stated goals "to isolate Israel economically, socially, and culturally" and encourage "comprehensive divestment" from Israel, all "while overlooking anti-Israel aggression".
Debate over how the church includes or separates LGBTQ people is dividing the United Methodist Church, including churches in Virginia.
The vote - though nonbinding - disappointed many delegates who had wanted to increase pressure on Israel to withdraw from lands it has occupied since the 1967 war that pitted it against Jordan, Egypt and Syria.
On Tuesday, the sound of demonstrators singing the hymn "Blest Be the Tie That Binds", their hands tied together with the colorful stoles LGBT supporters have worn throughout the conference, almost drowned out a motion by the Rev. Mark Holland asking bishops for direction on how to move forward on the issue of human sexuality.
Last week Hillary Clinton, the front-runner for the Democratic presidential nomination who was raised and remains a practicing Methodist, criticized the BDS movement in a statement that was believed to be directed at the church, though it did not specifically mention the church.
"It's life and death", she said, "and yet we're not ready, and I'm just caught in that tension".
BDS activists have scored a series of successes in recent years in advancing similar resolutions, most prominently the United Church of Christ in 2015 and the Presbyterian Church (USA) a year earlier.