Former Senator John Edwards of North Carolina is running third, a sharp setback in the state where he was born and scored a primary victory in his first presidential campaign four years ago.
The Associated Press made its call based on surveys of voters as they left the polls.
About half the voters were black, and four out of five of them supported Obama. Black women turned out in particularly large numbers. Clinton and Edwards each won roughly 40 percent of the white vote, with about 25 percent going to Obama.
The victory was Obama's first since he won the kick-off Iowa caucuses. Clinton scored an upset in the New Hampshire primary a few days later. They split the Nevada caucuses, she winning the turnout race, he gaining a one-delegate margin.