58-year-old Prachanda received 242 votes in favour and 114 against, failing to reach the magic figure of 301 to win the poll, weeks after Madhav Kumar Nepal of CPN-UML resigned as Prime Minister under Maoist pressure.
Four Madhesi parties, whose combined strength is 84, along with some other smaller parties abstained from voting, which started at 4 pm local time after a five-hour delay.
After ex-premier Prachanda's defeat, lawmakers were asked to vote for or against Nepali Congress candidate Ram Chandra Poudel, 65, who too crashed out of the race, receiving just 124 votes in favour and 235 against.
CPM-UML's Jhala Nath Khanal, 61, withdrew his candidature at the last minute, despite Maoists' assurance that they would support him in the election.
CPN-UML's Nepal said that his party would try to forge consensus with other major groups before the Friday re-poll which was necessitated after Parliament failed to elect a new Prime Minister.
Before the voting, Parliament Speaker Subash Nemwang announced the names of the candidates and allowed lawmakers to speak for or against them.
The country plunged into a political crisis last month after Nepal's resignation, following which major parties failed to arrive at a consensus candidate for the post of Prime Minister.
CPN-Maoist in the single-largest party with 238 MPs, while Nepali Congress and CPN-UML have 114 and 109 seats respectively in the Constituent Assembly.
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