Renu Dahal, who secured 43,127 votes, defeated her nearest rival - CPN-UML's Devi Prasad Gyawali - by 203 votes.
Gyawali got 42,924 votes and gave a tough fight to the daughter of CPN-Maoist Centre's chief.
Re-polling was conducted in Ward number 19 as per the court's verdict as counting of votes of Bharatpur Metropolis, under the second phase of local-level election, was put off after some people vandalised the ballot box.
Nepali Congress' Parvati Shah won the post of Deputy Mayor, beating her rival Divya Sharma Acharya of CPN-UML.
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Election was held earlier in the metropolis on May 14 in the first round of civic polls. However, some cadres had damaged the ballot papers on May 28 when vote counting was underway.
Prachanda in May resigned after a brief stint of nine months, honouring a power sharing understanding with the ruling coalition partner Nepali Congress to hand over the country's leadership to the largest party in Parliament.
His resignation cleared way for his former political rival and Nepali Congress president Sher Bahadur Deuba, who took over as the prime minister.