"It's about building a stronger, more cohesive society where we all accept that ... discrimination against children on the basis of whatever, including their sexual orientation, is no longer acceptable," McGuinty told reporters.
Thomas Cardinal Collins, Archbishop of Toronto, had accused the Liberals of infringing on religious freedom by amending the bill to say schools must allow students to use the word "gay"' in a club name.
Collins was not available for comment Tuesday, but released a statement on behalf of the Assembly of Catholic Bishops of Ontario expressing "serious concerns about certain aspects" of the bill.
"Recognizing that the Accepting Schools Act is now the law, Catholic partners will seek, as we have always done, in a way that is in accord with our faith, to foster safe and welcoming school communities," wrote the cardinal.
Catholic trustees had complained the legislation will force them to accept student clubs that go against their faith, but said Tuesday there were no concerns about implementing the new policy.
"We already have groups in existence that are at least attempting to meet the needs of kids in schools that are bullied for various reasons, so I don’t see a dramatic change other than in the name," said Kathy Burtnik, vice-president of the Ontario Catholic School Trustees' Association.
"There is no intention at this time to pursue any legal challenge."
McGuinty predicted Catholic schools would find ways to implement the anti-bullying bill.
"There is a lot of common ground here and there are values that transcend any one faith," he said.
"I am convinced that once we have this in place that Catholic schools, Catholic teachers, Catholic principals, Catholic parents will understand its true significance."
The NDP voted with the minority government, but the Conservatives opposed the Accepting Schools Act, saying the province has no business telling schools they must allow students to form clubs called gay-straight alliances.
"Our position is that principals run the schools with the parents and school boards, not students," said PC Leader Tim Hudak.
The New Democrats agreed with McGuinty that Catholic schools would implement the changes called for in the bill.
"There are lot of people from the Catholic community, including the union that represents the teachers, that support the legislation in the way that it passed today," said NDP Leader Andrea Horwath.
"We just have to make sure that the implementation happens and that kids are able to combat bullying of all kinds in their schools."
The Tories said the debate about gay-straight alliances overshadowed the bullying issue, and was an intentional effort by the Liberals to trigger a debate about funding Catholic schools in Ontario.
"I can only suppose that must have been quite deliberate on the part of the Liberals to open up that whole debate, because we're very clearly heading in that direction," said Christine Elliott, the Tories' deputy leader.
"It is a concern. We learned very clearly in the 2007 election that’s something that people feel very strongly about, and I don’t think we want to have another debate on religion in schools."
The Green Party of Ontario, which has no elected members, is the only political party calling for the abolition of separate schools, saying the province can't afford to fund two public school systems.
The legislation was not really about bullying in the end, but was an attempt to make the Tories look homophobic, said Elliott.
"It’s about trying to wedge us for their own political purposes and I think that's a great shame," she said.
The issue of protecting kids transcends partisan politics, said McGuinty, who stopped short of accusing the Tories of homophobia for voting against the bill.
The Conservatives' opposition to the anti-bullying bill "has everything to do with the fact that we’re going to be talking about gay-straight alliances in Ontario high schools," said McGuinty.
"I think they’re missing an opportunity to take a stand on behalf of our generation to say to all and sundry discrimination against people based on sexual orientation is not honoured in Ontario," he said.
The New Democrats pushed to have the Liberal bill amended to make sure students could use the word "gay" in the name of their anti-homophobia clubs.
"We were proud to stand up for a bill that's going to actually do what it needs to do, which is give those kids the clubs that they need to provide supports, so they don’t end up isolated and feeling lost and doing drastic things," said Horwath.
Some religious leaders who opposed the bill suggested it was the first step by the Liberals towards introducing a new sex-ed curriculum in schools after they were forced to withdraw the last attempt to update the policy.
Education Minister Laurel Broten rejected the idea.
"Let me be very, very clear Bill 13 has nothing to do with sex-ed," said Broten.
"If and when we embark on a conversation about sex-ed, we’ll have that conversation with Ontario parents."
The anti-bullying bill was the first piece of legislation passed by the Ontario legislature in more than a year, other than a routine supply bill to keep government functioning.