Bhattarai, who polled 340 votes to defeat his Nepali Congress rival R C Poudyal by 105 votes, is scheduled to take the oath of office at the Rastrapati Bhawan.
India educated Bhattarai, who has a doctorate from New Delhi's Jawaharlal Nehru University, won with the crucial support of the the Terai-based United Democratic Madhesi Front (UDMF), the alliance of Madhesi parties that is the fourth largest political force in the Assembly.
Accommodating some eight Madhesi parties in the cabinet will be a key challenge for Bhattarai. Sources said the Madhesi parties have demanded at least two deputy Prime Ministers' posts and a dozen ministerial portfolios during negotiations for providing support to the Maoists.
"Baburam Bhattarai secured 340 of the 574 votes cast, giving him a majority," Speaker Subash Chandra Nemwang announced after the voting in the House.
Bhattarai said his "government will make efforts to forge national consensus on key issues." The Maoists need the cooperation of all the parties to push forward the stalled 2006 peace process and the drafting a new constitution.
President Ram Baran Yadav had directed the Parliament to choose a new prime minister after Jhal Nath Khanal, who was elected premier after 17 rounds of polls in Parliament over a period of seven months on February 3, resigned on August 14 for failing to make "concrete" process in the peace process.
The Maoist rebels, who ended their decade-long insurgency in 2006, emerged as the single largest party during the Constituent Assembly election in 2008.