Witnesses said that police in armed gears intercepted the protesters at the entry point of the capital's diplomatic zone in Gulshan area as they moved towards the Pakistani mission.
Left-leaning Workers Party of Bangladesh, a coalition partner of the ruling Awami League, had organised the protest, which was joined by activists of Awami League student's front.
"They are trying to hatch a conspiracy... The mission must be shut down," Workers Party general secretary Fazle Hossain Badsha told the protesters at the rally.
Pakistan's harsh protest against the trial and execution of top 1971 war crimes convicts mostly from the fundamentalist JeI has angered Bangladesh, which has accused Pakistan of interfering in its internal affairs.
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Despite a coalition partner organising the rally, Prime Minister Sheikh Hasina was restrained in her comments at a press meet. She said Bangladesh will not sever diplomatic ties with Pakistan because of its support to the war criminals.
"Let Pakistan say what it prefers, diplomatic relations would be there... But their statement also made it clear that the war criminals acted as the agents of Pakistan and involved with the genocide with Pakistani Army," she said.
Bangladesh last month summoned Pakistan's envoy twice after Bangladesh High Commissioner in Islamabad was summoned there amid a continuing row over the execution of Nizami.
Pakistan foreign office had last month issued a statement saying Islamabad was "deeply saddened" over Nizami's execution.
The Pakistani national assembly in a simultaneous move had passed a resolution condemning the execution recalling that he was a former lawmaker and minister in the past BNP-led four-party government with Jamaat being its crucial ally.