The Bolton Refuge House is one of the local organizations that would have been affected, with officials saying they would have faced closing the transitional housing they run for domestic abuse victims.
Director Jerry Wilkie says taxing small non-profits would hurt the community more than the additional income would help.
"Those needs are still going to be there so (the community is) going to get those costs on another end at higher levels, so the end result would not have been a windfall for those communities," said Wilkie.
The Assembly passed the bill 90-9 early Friday morning, and the Senate had high numbers earlier this week when they passed the bill 32-1.
The legislature has a study group planned for this summer to determine whether some of the organizations initially targeted in the court case should be required to pay property taxes in the future.