Parker will replace term-limited Mayor Bill White on Jan. 1.
The New York Times reported on Saturday that Parker drew 53% of the vote, with all precincts reporting.
"The voters of Houston have opened the door to history," Parker told supporters after her victory. "I know what this win means to many of us who never thought we could achieve high office. But let us at this moment join as one community. We are united in making Houston the city it should be, could be, can be and will be."
The Gay & Lesbian Victory Fund – an organization devoted to advancing LGBT leaders in communities across the nation – celebrated Parker’s win in a statement on Saturday:
This is a watershed moment in American politics. Annise was elected by fair-minded people from across the city because of her experience and competence, and we're glad Houston soundly rejected the politics of division. This victory sends a clear signal that gays and lesbians are an integral part of American civic life, that we're willing to lead, and that voters will respond to candidates who are open and honest about their lives.
Parker, who ran primarily on a platform of budget reform, will fulfill her term as city controller before taking the mayor’s office on the first of the New Year.