Deuba, 70, was the sole candidate to contest in the prime minister election as the main opposition UML or any other party didn't register their candidacies.
He secured 388 votes in his favour and 170 votes against him. A total of 558 were cast during the voting. He needed 297 votes in the 593-strong Parliament to prove his majority.
The Nepali Congress leader has become the 40th Prime Minister of Nepal. The post of prime minister fell vacant after Maoist leader Prachanda resigned last month under a power sharing deal with the Nepali Congress leader.
Deuba is likely to form a small Cabinet tomorrow which will be expanded in a few days and some of the Madhesi parties are also likely to join the coalition. The responsibility of conducting the second phase of local level election will rest upon Deuba.
Deuba served as the prime minister from 1995 to 1997, from 2001 to 2002, and from 2004 to 2005. Deuba was sacked by the then King Gyanendra Shah in 2005 over failure to hold elections and bring Maoist rebels to a round table negotiation.