Pentagon officials say military chaplains can participate in private homosexual marriage ceremonies, whether on or off military installations.
The ruling announced Friday follows the lifting of the "Don't Ask, Don't Tell" ban on gays serving openly in the military.
Some congressional lawmakers have objected to the move, saying it would violate the 1996 Defense of Marriage Act.
The Pentagon said there is a provision for chaplains whose religious convictions forbid the marrying of gay couples.
The new rules say another chaplain may step in or a minister from the community to perform a gay marriage between service personnel.
"If your tenets of faith prohibits, then you are not forced to do it. No harm, no foul. If your faith allows it, you perform it. No big deal," Air Force Chaplain Ted Wilson said.
The Pentagon said same-sex marriages can only be performed by military chaplains in states where gay marriage is legal.