The Air Force One carrying Obama, his wife Michelle and top officials of his administration, took off around 9 a.m.
Foreign Secretary Nirupama Rao, Indian Ambassador to the US Meera Shankar and Union Minority Affairs Minister Salman Khurshid, who was the minister-in-waiting for the US president, were at the airport to see him off.
Obama flew into India Saturday, and spent a night in Mumbai, where he stayed at the Taj Mahal Hotel, one of the key targets of Pakistani terrorists in November 2008.
He flew into New Delhi Sunday for two hectic days of engagements.
Besides visiting and admiring the Humayun's Tomb with Michelle, Obama held talks with Prime Minister Manmohan Singh and addressed members of both houses of Indian parliament.
The US' declaration of support for India for a permanent seat in the UN Security Council formed the high-point of Obama's maiden visit to this country.
Indonesia is the second leg of Obama's four-nation Asia tour that will also take him to South Korea and Japan.