Obama told Modi that the largest democracy in the world had given a decisive mandate.
The US leader also expressed the hope that under Modi's leadership, India would play a significant role on the global stage.
In Washington, White House Press Secretary Jay Carney said the prime minister-elect is welcome to visit the US, which has denied him visa since 2005 in the wake the Gujarat riots.
Hours after the results of the elections were out, the White House exuded confidence that the India-US relationship under a Modi Government would make further progress.
"The Prime Minister of India will receive a visa to travel to the United States. We look forward to working with the new government and the new Prime Minister. I don't anticipate any problem in that regard," Carney said when asked about the visa issue.
"The prime minister of India will be welcomed to the US."
In 2005, the US State Department had revoked a visa that Modi had for travelling to the US on the ground of alleged human rights violations after the 2002 Gujarat riots. The US has repeatedly said there is no change in its long-standing visa policy relating to Modi but he is free to apply for a visa and await a review like any other applicant.
However, in a sudden u-turn in February, the US signalled the end of its boycott of Modi when its ambassador to India Nancy Powell met him in Ahmedabad.
"We congratulate Narendra Modi and the BJP on winning a majority of seats in this historic election. Once the government is formed, we look forward to working closely with the prime minister and the Cabinet to advance our strong bilateral relationship based on shared democratic values," Carney told reporters.
"The President will be reaching out to Modi. And as I noted, we congratulate him and the BJP on winning a majority of seats in these historic elections," Carney said as he described Indo-US relationship as "important".
He said Obama looks forward to building on the progress the two countries made during the outgoing UPA government led by Prime Minister Manmohan Singh.
"I think the future is bright. We have long said that we look forward to working with whomever the Indian people choose in these elections," the White House Press Secretary said when asked about the future of India US relationship.