Delegates narrowly voted down a proposal to add same-sex unions to national Church laws at the Church's general synod.
Branches of the Church in each province will however still be able to decide if they want to conduct same-sex unions.
Rev Linda Nicholls, who recently became the first woman chosen to lead the Church, acknowledged the disappointment the decision would bring for many.
"The failure of the motion to change the marriage canon will be deeply painful for LGBTQ+ members of our Church and for those beyond the Church who looked to this step as a sign of hope and inclusion," Bishop Linda wrote in a Facebook post.
The motion required the support of two thirds of delegates from the three orders - lay, clergy and bishops. 80 per cent of the lay delegates and 73 per cent of the clergy voted to adopt the resolution. However, the bishops were two votes shy of what was needed for the proposal to be written into Church law.
Bishop Linda said that when the decision was announced, the only sound in the room was the sobbing of a member from the LGBTQ+ youth delegation.
"That sound will resound in the hearts of all those present as a moment not only of personal mourning but of the mourning of a Church that was unable to find a way to live with differences despite the best efforts of many people," she added.
The Anglican Church of Canada has been debating whether to add same-sex marriage to its Marriage Canon for several years.
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