Shakeel had earlier filed nomination papers as a MQM (Haqiqi) candidate, but his papers were rejected by the Election Commission. He filed an appeal and was allowed to contest as an independent candidate.
"He was supported by the MQM and today's killing shows we are not being allowed to campaign," a spokesman for the MQM (Haqiqi) said. The MQM (Haqiqi) is a breakaway group of the dominant Mutthaida-e-Qaumi Movement, and represents the Urdu speaking population in Pakistan's biggest city.
Three people, including MQM(H)-backed independent candidate Shakeel Ahmed, were killed in a shootout between two rival groups, police said.
Police said shops and markets were been shut down as the situation turned tense in one of the city's most populous areas, Landhi, where the incident occurred. The Election Commission has suspended elections in two constituencies after the incident.
In another incident, a candidate of the PPP, contesting for a provincial assembly seat, went missing, leading to protests by party workers.