Farrakhan, 75, said that Obama's presidential candidacy had excited the nation in a way not seen since Robert Kennedy ran for the White House in 1968, and that he had been moved by the "oneness of spirit" he saw among voters, particularly on election night in Chicago.
But he said the country remained "divided and polarized," and he warned that the president-elect faced a daunting task in taking the reins of the nation during one of the most troubled periods in its history.
Many of the voters that backed Republican Senator John McCain "were older Americans and most reside below the Mason-Dixon line where racial attitudes and traditions die hard," he said in a reference to the American South.
"We can change laws, but it's difficult to change attitudes," he told a congregation of about 1,200 people at Mosque Maryam on Chicago's South Side.
He cited news reports that gun sales had surged since Obama's electoral victory, and told of how fights reportedly broke out in some schools, with white students chanting "white power," while blacks students chanted "black power."
"I'm sure that many of our people have unfortunately lost their lives because of the absolute hatred that is manifested now that one of our own has risen to such a high office," he told the crowd at the national headquarters of the Nation of Islam.
Farrakhan is the leader of the religious group which rose to national prominence under Malcolm X during the civil rights movement.
He has been an influential voice but often a lightning rod for criticism with his incendiary remarks prompting charges of anti-Semitism and homophobia. He made headlines with his accusations that the government deliberately blew up levees in New Orleans after Hurricane Katrina in an attempt to wipe out the city's black population.
On Sunday, he also said that the gracious concession speech given by McCain had not assuaged "the pain of loss and frustration and disappointment to those who felt great pain at Obama's rise."
And he said that for some people, the prospect of a black family in the White House, was a "sacrilege."
But he said Obama had reached out to those voters who did not cast a ballot for him, pledging to earn their support and represent them too.
Farrakhan heaped praise upon Obama during the long speech, and said he could speak openly now that the election was wrapped up and his comments could not be used to hurt the Illinois senator.
He never formally endorsed Obama during the long campaign, apparently conscious that such a step might handicap the aspiring presidential candidate given Farrakhan's divisive reputation.
On one occasion during the battle for the Democratic party nomination, Farrakhan did speak in glowing terms of the Obama, saying he was the only man who could heal the racial divisions in the United States and that he carried the hopes of the "entire world" for a better America.
But shortly afterwards, during a televised debate with his primary opponents in February, Obama distanced himself from the controversial leader of the Nation of Islam, saying he had publicly disavowed Farrakhan's anti-Semitic comments, and had not sought his support.