Hospital doctors confirmed that three bystanders were killed and about 20 people injured in the 20-hour mutiny.
Fifty women and children, who had been stranded at the BDR headquarters when thousands of guards mutinied against their superiors over pay, were freed as the guards surrendered their arms.
The mutineers agreed to lay down their arms after Sheikh Hasina, the prime minister, met a group of them at her residence on Wednesday and offered them amnesty.
The prime minister also pledged to look into their demands for better pay.
Wednesday's unrest saw the guards seize their headquarters and a nearby shopping mall, and trap dozens of children in a school.
The army was called in and shut down nearby streets as helicopters kept watch over the area.
Intermittent gunshots rang out for more than four hours, while black smoke billowed from the BDR compound.
The guards said they were upset with their superiors for not raising long-standing demands for equal pay and working conditions as army soldiers during Hasina's visit the previous day.
Kailash Budhwar, a London-based South Asia analyst, told Al Jazeera that the mutiny was "most unexpected".
"And it happened from a unit that was supposed to be most disciplined ... a paramilitary force who guard the border," Budhwar said.
"This certainly brings to memory the dark days when there was turmoil and anti-social takeover, and there are other undercurrents in Bangladesh who might take advantage of the situation."