Ahn Cheol-soo, who unsuccessfully ran in the 2012 presidential election, defeated Huh Joon-young of the ruling Saenuri Party in Seoul's Nowon C district.
Ahn garnered 60.5 percent of the eligible votes, while Huh won 32.8 percent.
Independent Ahn's victory triggered speculation that he and his followers may create a new party ahead of the local elections next year, which is considered a serious threat to the main opposition Democratic United Party (DUP).
Analysts said the high popularity that former software entrepreneur Ahn has enjoyed illustrates the public disillusionment with the political establishment mired in old-fashioned politics.
The so-called Ahn Cheol-soo phenomenon is a wakeup call for ugly politics in a country where people are tired of ceaseless factional or partisan fighting, they said.
Kim Moo-sung of the ruling party won the by-election in the Yeongdo district, Busan, while Lee One-koo of the same party won the race in the Buyeo-Cheongyang district in South Chungcheong Province.
In Yongdo, Kim clinched 65.7 percent of the eligible votes against 22.3 percent for Kim Bi-oh of the DUP.
In Buyeo-Cheongyang, Lee and Hwang In-suk of the DUP garnered 77.4 percent and 16.9 percent of the vote, respectively.
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