The Utah-based church's support ahead of Tuesday night's vote came despite its steadfast opposition to gay marriage, reflected in the high-profile role it played last year in California's ballot measure that barred such unions.
"The church supports these ordinances because they are fair and reasonable and do not do violence to the institution of marriage," Michael Otterson, the director of public affairs for The Church of Jesus Christ of Latter-day Saints said.
Passage made Salt Lake City the first Utah community to prohibit bias based on sexual orientation or gender identity. Under the two new ordinances, it is illegal to fire someone from their job or evict someone from their residence because they are lesbian, bisexual, gay or transgender.
Utah lawmakers tend to quickly fall in line when the influential church makes a rare foray into legislative politics. So Tuesday's action could have broad reaching effects in this highly conservative state where more than 80 per cent of lawmakers and the governor are church members.
"What happened here tonight I do believe is a historic event," said Brandie Balken, director of the gay rights advocacy group Equality Utah. "I think it establishes that we can stand together on common ground that we don't have to agree on everything, but there are lot of things that we can work on and be allies."
But the church has pointed out an inherent dispute it has with the gay lifestyle. Mormonism considers traditional marriages central to God's plan. Gays are welcome in church, but must remain celibate to retain church callings and full membership.
It's strong support for Proposition 8 in California last year drew a sharp reaction from gay rights supporters nationwide, with many protesting outside temples that singled out Mormons as the key culprits in restricting the rights of gay couples.
Since then, however, Utah's gay community has sought to engage church leaders in quiet conversations to help foster better understanding, said Valerie Larabee, executive director of the Utah Pride Center.
"I thought this conversation would never come to be while I was here in Salt Lake City," said Larabee, adding that the discussions have "shifted her perspective of what's possible" and could foreshadow a different relationship between the two sides.
But addressing the council on Tuesday, Otterson said the endorsement is not a shift in the church's position on gay rights and stressed it "remains unequivocally committed to defending the bedrock foundation of marriage between a man and a woman."
Church support for the ordinances is due in part to the way the legislation was drafted to protect those rights. Exceptions in the legislation allow churches to maintain, without penalty, religious principles and religion-based codes of conduct or rules.
"In drafting these ordinances, the city has granted common-sense rights that should be available to everyone, while safeguarding the crucial rights of religious organizations," Otterson said Tuesday.
Previous Utah legislation that sought statewide protections for the gay community did not contain those exceptions.
And although this was the church's first public endorsement of specific legislation, it is not the first time the church has voiced support for some gay rights. In August 2008 the church issued a statement saying it supports gay rights related to hospitalization, medical care, employment, housing or probate as long as they "do not infringe on the integrity of the traditional family or the constitutional rights of churches."
Last year, church leaders were silent on a package of gay rights bills known as the Common Ground Initiative, dooming them from the start.