Matt Schaefer said he was deliberately prevented from taking part when the bread and wine passed him by at St John's Evangelical Lutheran Church in the Canadian city of Warman, Saskatchewan.
Mr Schaefer said the incident was "so embarrassing" and that he contacted the church's pastor in October for clarification about the incident.
He told Canadian broadcaster CBC News: "He called me, eventually.
"He asked me if I remembered confirmation class and the part on homosexuality."
Mr Schaefer, who has been in a same-sex relationship for four-and-a-half years, attended St John's in his younger years and remains a member.
He had been joining relatives at the church for a family wedding when the alleged incident happened.
In a statement seen by CBC News, Rev Randy Heide said his church holds on to traditional teaching on "all matters of life and faith".
He added: "I sincerely care for and pray for this young man whom I have known and served periodically since high school.
"I have encouraged him to seek out a church in his community which would be able to regularly serve his spiritual needs.
"I continue to pray for the Lord's hand of guidance upon him."