The former first couple witnessed the private ceremony on Saturday in Kennebunk between Bonnie Clement and Helen Thorgalsen, according to Jim McGrath, a Bush spokesman.
Clement posted a photograph on her Facebook page of President Bush signing a piece of paper as the couple, close friends of the Bushes, watched and held champagne glasses.
The couple owns H.B. Provisions, a general store in Kennebunk, Maine. The former president owns a compound in Kennebunkport, about four miles (six km) east of Kennebunk.
Maine is one of 13 states that allows gay marriage.
In June, the U.S. Supreme Court threw out a key part of the Defense of Marriage Act, which barred same-sex couples from federal marriage benefits. But the high court declined to rule on whether gay men and lesbians have a fundamental right to marry, leaving it to states to decide.
The ruling has led to legal challenges in federal and state courts to laws that restrict the rights of gays and lesbians.
Several other notable Republicans have voiced support for gay marriage, including former Vice President Dick Cheney and Ohio Senator Rob Portman.
But same-sex marriage is opposed by most Republicans. A Gallup poll in July found 66 percent of Republicans were against making same-sex marriage legal in all 50 states.
Republican National Committee Chairman Reince Priebus reiterated in July the party's stand that marriage was between one man and one woman.
(Reporting by Brendan O'Brien; Editing by Ellen Wulfhorst and Eric Beech)