Awab Alvi said he believed MQM thugs were behind the irregularities in the constituency.
The other two parties are the Pakistan People's Party (PPP) and the Muttahida Qaumi Movement (MQM).
Pakistan's governing coalition held 181 seats - including the MQM's 25 - in the 342-member parliament.
Local Pashtun activists say Karachi's largest party, the MQM, is behind most of the violence.
In part, the MQM walked out in opposition to a planned hike in the oil price.
The MQM dominates politics in the city of Karachi, the capital of the southern province of Sindh.
The MQM has threatened to quit the federal government, which could reduce it to a parliamentary minority.
The MQM quit the coalition on Sunday, condemning last month's 9% rise in the price of petrol and kerosene.
MQM, which draws support from those, or their kin, who left India at the time of partition in 1947.
Followers of the MQM, a party dedicated to Karachi's Urdu-speaking muhajir community, were in the thick of the killing.
The MQM - which took most of the seats in Karachi - denies any irregularities and is boycotting the vote.
Altaf Hussain, leader of the MQM party that controls Karachi, addressed supporters from London last Sunday after Pakistan's general elections.
BBC: Pakistan MQM's Altaf Hussain attracts UK police interest
On Sunday, several hundred demonstrators against MQM gathered outside 10 Downing Street, the London residence of the British prime minister.
The MQM's departure leaves Mr Gilani's Pakistan People's Party (PPP) well below the 172 seats needed to preserve its majority.
The MQM, which withdrew two ministers from the federal cabinet last week, was the second largest party in the coalition.
Sunday's partial re-run of the vote in Karachi was ordered after Mr Khan's party accused the MQM of widespread vote-rigging and intimidation.
On Monday, a senior MQM leader blamed the violence on gangs of extortionists and land grabbers who had taken the city hostage.
MQM, as a result of attacks on itself by a breakaway faction.
Since the mid-1980s, the MQM has won every poll it has contested in Karachi and it did so again in last Saturday's general election.
BBC: Pakistan MQM's Altaf Hussain attracts UK police interest
This bout arose ahead of a by-election necessitated by the murder of a leading provincial lawmaker, a member of the Muttahida Qaumi Movement (MQM).
Mr Khan, a former cricketer, said he also held the UK government responsible, as he had already given a warning about the MQM leader's remarks.
Most shopkeepers in the area belong to the Urdu-speaking community that traditionally supports the MQM, which is part of the governing coalition in Sindh province.
But there have also been separate battles over turf between the city's Baloch community - the original inhabitants of the city - and the MQM.
Even so, he said that by not pulling out of government in Sindh province, the MQM had given the government "a chance to take corrective measures".
Fixing Karachi will require Sharif to garner the support of MQM, PPP, and ANP -- none of whom at this point look poised to join his government.
As for the MQM, it has its main base in Karachi, and is reported to have a strong militant wing of its own, a claim it denies.
As the National Assembly holds its first session of the new year later on Monday, the MQM is expected to cross the aisle to the opposition benches.
The MQM (Muttahida Qaumi Movement) is supported mainly by Muslim Urdu-speaking people whose families moved to Sindh province at the time of the partition of India in 1947.
BBC: Pakistan MQM's Altaf Hussain attracts UK police interest
However, Mr Rehman Malik categorically denied that MQM was involved.
The MQM is based in Sindh province, with a membership mostly comprising the descendants of Urdu-speaking migrants to Pakistan at the time of the partition of British India in 1947.
BBC: Pakistan's MQM party shuts Karachi offices after attack
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