The vote comes in the wake of an emotional debate to ban gay marriage in the state constitution that was derailed earlier this session.
Tim Orient, who lives with his husband and two children in Indianapolis, was married five years ago in Massachusetts. If the bill passes through final legislative negotiations and is signed by Gov. Mike Pence, Orient will have to file jointly for his federal return then split his assets for the state.
"I guess it was something I'd figured I'd have to live with," Orient said. If Indiana keeps the split with federal policy, "it's going to cost us twice as much" to file his returns, he said.
Without the changes to the bill, Indiana could have adopted a new Internal Revenue Service policy giving same-sex marriages equal privileges in tax filings.
Supporters say the change was necessary to match Indiana's ban on gay marriage, while opponents say it's another instance of discrimination against same-sex couples by the Legislature.
"The revenue code is not the appropriate place to have that discussion," said state Sen. Brandt Hershman, R-Buck Creek. "We would be adopting that policy without any legislative action to back it up."
Monday's amendment — made the day before the Senate vote — denied an opportunity for public input, Indiana Equality Action President Chris Paulsen said. The group was one of several that also opposed the proposed constitutional gay marriage ban.
"It would've been productive to have a candid and meaningful discussion in which the public could participate," Paulsen said in a statement. "We'll hope for a resolution for this matter."
Hershman said a late catch of the new IRS policy, which was established Aug. 29, 2013, after the U.S. Supreme Court's ruling against the Defense of Marriage Act, led to the delayed amendment.
Adopting federal policy would have meant thousands could have avoided filing multiple tax statements before the April 15 deadline, Paulsen said.
Keeping the status-quo policy on same-sex taxes will bring "backlash," said Henry Fernandez, who lives with his partner and two children in Indianapolis but is not married.
"Inevitably there will be a federal suit that will be filed on behalf of Indiana same-sex couples," Fernandez said.
But Hershman and others say recognizing same-sex marriage in state taxes would have caused a rift with the state's current ban on gay marriage.
"Without a constitutional amendment protecting marriage," said Micah Clark, the executive director of the American Family Association of Indiana, "the state has to be very careful not to enact policies that undermine traditional marriage, which activists wanting same-sex marriage could then use to cause a judge to overturn our marriage laws."
The House has already passed the broader tax bill. Because it was amended in the Senate, it will now go to a conference committee.