Supporters of the ban argued that removing the language would set the state up for a court challenge delaying the constitutional ban.
"I believe HJR 3, as written, is the right public policy for the state of Indiana," said Rep. Eric Turner, R-Cicero, and the author of the marriage ban. "The second sentence simply prevents marriage by any other name."
But the sentence has been a sticking point for many lawmakers, including some who have said they otherwise support banning gay marriage.
Opponents have argued that the civil union language could prevent employers from offering benefits to same-sex couples.
Indianapolis resident Norman Sider carried a water bottle emblazoned with the Freedom Indiana logo - the umbrella group opposing HJR 3 - and said he was heartened by the bipartisan support.
"This is just the beginning, but it was a successful beginning," Sider said after watching the vote. "How this will turn out? I don't know. But I would hope that both (House and Senate), when they have a chance to vote, will again be very bipartisan."
As opposition to the more expansive ban coalesced, one of the strongest Republican supporters of the proposed ban appeared to take a step back.
House Speaker Brian Bosma, R-Indianapolis, took a lead role in pushing the measure out to the full House of Representatives. But he said Monday's vote fulfilled his priorities on the issue.
"My goals have been met in full," he said. "I had two commitments: One, that the entire body would have the chance to vote on it. And two, that I wouldn't ask anybody to vote any way other than their conscience."
Republican Gov. Mike Pence has taken a sharper stance, saying he prefers to see the issue settled this year. Pence made a plea to lawmakers in his second State of the State address earlier this month.
The House could send the measure to the Senate as soon as Tuesday, setting up the second major phase of the legislative battle. Senate President Pro Tem David Long, R-Fort Way ne, has said the measure would be vetted by the Senate Judiciary Committee.