PTI's Arif Alvi secured 77,659 votes to beat MQM's Khushbakht Shujaat who polled 30,365 votes, according to the Election Commission of Pakistan (ECP).
MQM, Karachi's dominant party, has captured majority seats in national assembly and provincial assembly elections in Karachi since the late eighties. In the May 11 general elections, MQM managed to bag 18 national assembly seats.
The repoll in 43 polling stations out of 180 in the constituency was ordered following allegations of vote-rigging in the upmarket district of Pakistan's biggest city during the general election.
The result came as a setback for the MQM which had earlier ridiculed the low turnout in the re-polling held one day after the brazen killing of PTI's senior vice-president Zahra Shahid Hussain outside her residence on Saturday night.
The NA-250 and re-polling on two other provincial seats became a flash-point between the PTI and MQM, which boycotted the re-polling.
The MQM took out big rallies in different parts of the city today to protest Imran's statement about holding MQM chief Altaf Hussain, who lives in exile in London, directly responsible for the death of its vice president. The big rallies led to markets closing down in the Saddar area out of fear while traffic was clogged up as many roads were closed by law enforcement for security reasons.
The PTI and Jamaat-e-Islaami also staged protest sit-ins in some areas demanding re-elections at all the constituencies in Karachi as they accused the MQM of vote-rigging.
The MQM and Pakistan Peoples Party (PPP) had also announced to boycott the re-polling after the ECP rejected their demands of a re-do for the entire constituency.
Alvi told reporters that his victory was just the tip of the iceberg and PTI candidates had also done well in other constituencies but there was mismanagement and rigging at many polling stations in other areas.
"I think my victory shows that the people of Karachi want a change, they want peace and tolerance and to make this city the business and financial hub it once was," he said.