Rajapaksa, who turned 65 yesterday, was sworn in at a colourful open air ceremony held at the sea front, by the chief justice Ashoka D Silva.
The Sri Lankan leader who led the country's triumph over 30 year-old-insurgency was reelected President by an overwhelming majority in the January 26 elections.
He called the election two years early to cash in a soaring ratings in the wake of last year's military victory over the Tamil Tiger.
In September, Rajapaksa government passed an amendment to the constitution to eliminate term limits for the presidency.
A tri-service march past by thousands of troops marked the ceremony which was telecast live and the Lankan capital wore a festive look for the occasion for which a public holiday had been declared.
Security was tight for the ceremony in the capital which was boycotted by the opposition United National Party and the Marxist-Leftist JVP, both backers of the defeated candidate and former army chief Sarath Fonseka.
"We take this decision to mark our protest to the exhorbitantly expensive ceremony," deputy leader of the UNP Karu Jayasuriya said.
In his second reincarnation, a powerful Rajapaksa has said he wants to turn his island nation into a "wonder of Asia" and has announced a series of infrastructure projects, including a USD 1.5-billion port built by the Chinese in his hometown of Hambantota which he inaugurated yesterday.
"When I came to power I promised an honourable peace and a new Sri Lanka and I will keep my promise," Rajapakse said at the opening ceremony.
While pursuing development, he has shrugged off pressures by the West to link investments to human rights and turned to countries like Iran, Libya and China for help.
He also rejected allegations that the Sri Lankan army may have been responsible for substantial civilian deaths during its final offensive against the LTTE and dismissed calls for a international investigations into possible war crimes.