The church's pastor, the Rev. Calvin Butts, said he had fielded calls from people who wondered why he, a black man, was endorsing a white woman instead of Obama, who also is black.
"I would like to make one thing very clear," Butts said. "This was not and is not and will not become a race-based decision for me. And I hope that it has not and will not become a race-based decision for you, either. I respect Senator Obama. I applaud him, and I love him as my brother. But a vote for Hillary is not a vote against Barack Obama or any community, be it African-American, Latino and others for that matter."
As Clinton and Butts spoke, a few dozen sign-waving Obama and Clinton supporters competed with chants of "Harlem for Obama!" and "Hillary!"
Clinton said earlier that she was pleased to attend services at Abyssinian on the eve of the holiday celebrating the Rev. Martin Luther King Jr., whom she heard speak as a member of her church youth group in 1963.
"It was a transforming experience for me," she said.
She received a standing ovation at the church, which was founded by Ethiopian sea traders 200 years ago.
Clinton came under fire earlier for saying King's dream of racial equality was realized only when President Lyndon B. Johnson signed the Civil Rights Act of 1964. She has since reiterated her admiration for King.
"The 'I have a dream' speech is one of the great speeches that has ever been delivered in the history of the world," Clinton said Sunday.
Clinton and Obama divided the spoils in Democratic caucuses in Nevada on Saturday: She won the popular vote, he won the delegate contest.
Clinton, a New York senator, garnered support from women and made a strong showing among Hispanics. But Obama, of Illinois, won among blacks, who could make up more than half of the voters in the upcoming South Carolina primary.
Butts, a longtime power broker who also is president of the State University of New York's College at Old Westbury, stressed Clinton's experience in public life.
"A vote for Hillary Clinton is a vote to elect someone who has proven through time to me and to this community and this country that she has the experience to make things happen," he said.
Clinton said Democrats have an "extraordinary opportunity" to choose between worthy candidates.
"I respect the choices made by every voter," she said. "And I recognize what a challenging choice this is."
