Bishop Melvin Talbert and Pastor Val Rosenquist married two men in North Carolina on Saturday.
The pair risk being defrocked after breaking the rules when they allowed the men, one of whom had been attending the church for over 20 years, to wed.
Jim Wilborne and John Romano, both 52, kept the wedding a secret to prevent "people having time to organise a protest".
They hired security guards for the church.
Bishop Melvin Talbert was arrested alongside Martin Luther King Jr in 1960 and is known for his activism.
Speaking before the ceremony he told Buzzfeed News the church's views on homosexuality were "immoral, unjust, and oppressive, and they no longer deserve our loyalty and support."
Pastor Rasenquist added: "It's time to make a stand. I am willing to face whatever consequences I encounter. I am totally at peace with this decision."
The United Methodist Church, the US's largest Protestant denomination, is due to discuss allowing its pastors to conduct gay marriages in May.