Still, opposition remains strong in the House.
Rep. Tim Huelskamp, R-Kan., sponsor of the amendment, said he wanted to ensure that "America's military bases are not used to advance a narrow social agenda."
His measure would block funds to train the Chaplain Corps on the new policy. Huelskamp said the intent was to prevent chaplains from performing same-sex marriages, especially on Navy bases.
"What will happen to chaplains who decline to officiate over same-sex ceremonies?" Huelskamp asked. "The directive states that chaplains `may' perform same-sex civil marriage ceremonies. I fear that chaplains who refuse to perform these ceremonies may find themselves under attack and their careers threatened."
Last month, New York became the sixth state, joining Iowa, Connecticut, New Hampshire, Vermont and Massachusetts, to legalize gay marriage along with the District of Columbia.
Separately, a federal appeals court in California this week ordered the U.S. government to immediately cease enforcing the ban on openly gay members of the military.
Opponents of the amendment argued that more than 1 million members of the military have been trained on the new standard and Pentagon leaders see no adverse impact on the force.
Rep. Norm Dicks, D-Wash., said the measure simply tries to delay implementation of the law. Rep. Jared Polis, D-Colo., one of several openly gay members of Congress, said it was "an offense to the military to second guess their training for chaplains."
The vote's practical effect is unclear. The ban is likely to be lifted before Congress completes the defense spending bill for the budget year beginning Oct. 1.
The overall House bill must be reconciled with a still-to-be completed Senate version.