The House stripped that language from the amendment before passing it last month, and the Senate's decision not to restore the language before voting Thursday means the effort to amend the constitution must start fresh.
Indiana requires constitutional amendments to be approved in the same form in two consecutive biennial meetings of the General Assembly. The ban with the civil unions language first passed in 2011 and had seemed a slam dunk this year in the Republican-controlled Legislature. That would have set up a statewide vote in November.
But opponents began organizing early last year and lined up powerful names in the state's business and higher education communities to support their arguments.
Supporters of the ban said it was needed to prevent courts from overturning Indiana's law defining marriage as between a man and a woman. But they struggled to find their footing after House lawmakers stripped the civil unions language.
Republican Sen. Mike Delph had offered an amendment that would have restored the language, but he said he did not call it because there wasn't enough support for it to pass.
Republican Gov. Mike Pence lobbied for a November vote on the ban in his State of the State address and at a rally of ban supporters but later said he was removing himself from the legislative debate.
Senate Pro Tem David Long said the soonest a public vote on the amendment could be held now is 2016.