Vicar Mark Hood described it as a divisive issue for Christchurch, whereby other synods stood more firm in other regions.
However the vote passed in favour of backing a move for the church to authorise same sex marriages with 107 votes for yes, and 71 for no.
Hood said he was disappointed with the vote.
"The Bible is pretty clear, sex is a gift from God for a man and a wife."
He described the official vote in May as set to be a "watershed" moment however, regardless of which way that vote went. Individual churches within the synod would retain their own stance over whether to bless same-sex marriage.
The vote was welcomed by the St Columbia Anglican Church in Auckland's Grey Lynn. On Facebook it posted the vote was "good news...in a slow edging towards equality for same sex couples".