Thousands of supporters and workers participated in the rally where senior MQM leaders criticised the BBC for a recent documentary that they described as "baseless propaganda" against Hussain.
The documentary said that UK prosecutors had asked Pakistan to trace two suspects believed to have been involved in the murder of senior MQM leader Imran Farooq.
"The BBC documentaries are propaganda aimed at Altaf Hussain's character assassination, and a conspiracy against Pakistan's survival and stability," party leader Farooq Sattar claimed.
Some MQM leaders said the rally was held to remind the party's detractors that it still has control over Pakistan's biggest city and would not tolerate any conspiracy against its chief.
The party also held rallies in other parts of the country.