The guards agreed to surrender after the government promised them an amnesty and agreed to look into their demands for better conditions.
But the process stalled and was only completed Thursday after the government sent tanks into the capital in a show of force.
Government negotiator Mahbub Ara Gini said "all the mutinous border guards have surrendered their weapons."
The tanks rolled into the capital hours after the prime minister warned the guards she would "do whatever is needed to end the violence."
The revolt by border guards angry over pay left at least 10 people dead.
The private television station Channel 1 reported that nine tanks had taken up positions in a residential neighborhood near the compound seized by the guards Wednesday, while another correspondent said he saw at least seven more tanks heading toward the city.
The move came shortly after Prime Minister Sheikh Hasina appealed to the mutineers to surrender in a televised speech to the nation.
"We don't want to use force to break the standoff," Hasina said. "But don't play with our patience. We will not hesitate to do whatever is needed to end the violence if peaceful means fails."
Border guards first mutinied Wednesday at the group's headquarters in Dhaka, turning their weapons on senior officers, seizing a nearby shopping center and trapping students in a school on their compound. The guards later agreed to surrender after the government said it would grant them amnesty and discuss their grievances.
Mutineers fired shots at the commanding officer's residence at a border guard post in the southern town of Tekhnaf early Thursday, sending him fleeing, said police official Jalal Ahmed Chowdhury. Witnesses said violence also erupted at border guard posts in Cox's Bazar, Chittagong and Naikhongchari in the south, Sylhet in the northeast, Rajshahi and Naogaon in the northwest.
At least 10 people have been confirmed dead in Dhaka, but officials fear up to 50 people may have been killed there. On Thursday morning, the bodies of seven border guards - two of them of officers - were found outside the violence-wracked headquarters of Bangladesh Rifles, doctors at a local hospital said.
The insurrection was the result of longtime frustrations over pay for the border guards that didn't keep pace with that of the army's - highlighted by rising food prices in the chronically poor South Asian country as the global economic crisis grows.