In the call, on Monday evening US time, Obama congratulated Najib and reaffirmed "strong bonds of friendship between the United States and Malaysia," a White House statement said.
"The president noted that Malaysians had turned out in record numbers to vote and welcomed the prime minister's efforts to address concerns about election irregularities."
Malaysian opposition leader Anwar Ibrahim has pledged to produce evidence from the closest-ever polls in the country that he says will show the government is "illegitimate."
As part of a new focus on Southeast Asia, the Obama administration has reached out to Najib to improve relations with Malaysia, which were uneasy during the 1981-2003 rule of firebrand Mahathir Mohamad.
Anwar, who spent six years in prison on charges he said were trumped up by Mahathir over a power struggle, has also been a frequent visitor to Washington as he tried to cast himself as a voice of democracy and moderation.