The change in the rules follows demands by the American Civil Liberties Union on behalf of an inmate who sought a visit from his domestic partner. He cited a 2003 state law giving registered same-sex couples the same rights as married heterosexuals.
ACLU lawyer Alex Cleghorn said he first wrote officials a year ago about Vernon Foeller, who was in prison for attempted burglary. "It took several letters written from our office pointing out that they were breaking the law," he said.
The ACLU says prisons in Canada allow same-sex conjugal visits and that California appears to be the first U.S. state to take this step.
"It doesn't affect that many people," said Terry Thornton, a spokeswoman for the California Department of Corrections and Rehabilitation.
"We started this process because of the legislation, the California Domestic Partner Rights and Responsibilities Act of 2003," she said. "Basically no person or agency in the state can discriminate against any person or couple on the grounds that that person is a registered domestic partner or a spouse."
Gay sex outside of conjugal visits is still banned in California prisons, and inmates who marry in prison or same-sex couples in prison are ineligible for the visits.
Under the program, an inmate is allowed to live in a small apartment or trailer within the prison grounds for up to 72 hours with a spouse or partner or immediate family members. Visitors are allowed to bring up to 10 condoms.
Guards occasionally drop by to make sure the inmate has not escaped or caused harm.
Prisoners may cook in the units, and at Mule Creek State Prison northeast of San Francisco, they can choose from a menu that includes Hungryman Mexican Dinner ($3.99) and a Celeste Pepperoni Pizza ($2.49).
"Inmates have to stay within certain disciplinary guidelines and criterion to be involved in the program and so in that sense it assists me in assuring that my inmates are following the appropriate rules and regulations," Richard Subia, Mule Creek's warden, told Reuters.
Conjugal visits of any kind anger some state lawmakers, but bills in recent years seeking to bar them have failed. They are not allowed for inmates on death row or serving a sentence of life without parole, as well as those convicted of sex crimes and other violent acts.
At Mule Creek, which houses 3,788 inmates, 114 family visits have taken place this year in four trailer units in a separate prison yard, prison officials say.
The California prison system allowed Foeller the first same-sex conjugal visit in December, even though the formal change in the rules is still pending, officials said.
Only a handful of U.S. states, including New York and Mississippi, allow conjugal visits to married couples.