The re-poll of an eligible 86,316 voters was ordered in 43 polling stations in the upmarket south districts here under a constituency known as NA-250 following allegations of vote-rigging during the landmark general elections on May 11.
Although around 5,000 security personnel including police, rangers and military were deployed inside and outside the polling stations, the turnout remained extremely low, local media reported.
ECP spokesman said that officials had supervised the balloting, which they said went smoothly throughout the day without any hitch.
Polling was marred by strong protests by the MQM workers in Karachi and Hyderabad, as PTI chief Imran Khan blamed the murder of Zahra Shahid Hussain (59), vice president of the party's women's wing, on MQM chief Altaf Hussain, who lives in exile in London.
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"The low turnout is because the Election Commission of Pakistan should have given more time for re-polling. There was confusion among the people whether the re-polling will be held after the murder of Zara Shahid last night," a PTI supporter said in Delhi colony.
But police officials at different stations said the low turnout was also because of firing incidents in the city since night and protests in some areas.