"We believe that Catholic schools will be able to work with the legislation passed in the legislature," said the Alberta Catholic School Trustees Association in a news release issued Wednesday.
"Every child is a child of God who is valued and respected and every child will continue to have a place where they feel welcome as an important member of our community."
The alliances are peer-support groups for gay students aimed at making them feel welcome and at helping to prevent them from being bullied.
There are 94 such clubs in schools in Edmonton and Calgary, but none in rural areas or in faith-based schools.
On Tuesday, politicians of all stripes voted to pass an amended bill allowing such peer-support networks in all schools.
Only two member of the legislature, PC members Ian Donovan and Bruce Rowe, voted against it.
The issue had divided politicians for more than a year and Catholic school leaders previously resisted allowing gay-straight alliances in their schools.
Late last year, Premier Jim Prentice and his Progressive Conservatives shelved a previous version of the bill after critics said it would allow schools to segregate gay students off school grounds.
The revised bill also amends a controversial section of Alberta's human rights act that allows parents to pull students out of class when sexual orientation is taught.
Critics have said the "sexual orientation" phrase stigmatized the gay community by implying it was a topic to be shunned.
Liberal Laurie Blakeman, one of the opposition members who forced a decision on the issue by introducing a private member's bill last year, said Wednesday that while the vote is a victory, the work is just beginning.
"This is where the rubber hits the road to see whether the government resources it and whether they ensure compliance because people will try and get around it no question," said Blakeman.
"This is how we sort of test it and make it a living document."