The legislation passed by a vote of 149-137, with the crucial support of 16 Conservatives, including four cabinet ministers.
The bill now goes to the Senate which is unelected and essentially approves the House of Commons vote making it law.
It was one of the first tests of the Conservative caucus’ resolve on gay and transgender rights in Canada at a time when Foreign Affairs Minister John Baird has been mounting a strong defense of such rights abroad.
Opposition parties were united in their support for the bill, sponsored by New Democrat Randall Garrison.
“Today, New Democrats are proud to have contributed to ensuring equal protection under the law from discrimination and hatred based on gender identity,” Garrison said in a statement after the vote.
“Transgender and transsexual citizens are among the most marginalized and are too often victims of harassment and acts of violence.”
The bill had triggered vigorous, sometimes emotional debate in the Commons.
Some Conservative MPs opposed the bill on the ground it would allow pedophiles to lurk in public bathrooms.
“These constituents feel that it is the duty of the House of Commons to protect and safeguard our children from any exposure and harm that would come from giving a man access to women’s public washroom facilities,” Calgary MP Rob Anders said.
The Canadian Human Rights Tribunal had supported adding transgender identity to federal anti-discrimination and anti-hate legislation, saying it would promote acceptance and send a message about tolerance.
While some MPs argued that the transgendered were already protected on the basis of sex and disability, the tribunal said it would be better to have explicit protection so that the question is not perpetually challenged.