In an operation carried out early Wednesday in Karachi's Surjani Town area, police arrested Bashir Leghari, suspected of being the mastermind of the attack on the judge's convoy last month, along with two of his accomplices, said DIG South Dr Ameer Sheikh.
The operation was carried out with the help of of an intelligence agency, said the senior police official.
Leghari was injured in the exchange of fire during the operation, while a policeman was also wounded, he said.
The suspect is said to belong to the 'Asif chotu group' of the Lashkar-i-Jhangvi, a banned militant outfit involved in several sectarian killings.
On June 26, a powerful bomb explosion had targeted Justice Baqar's convoy as it was passing through the busy Burnes Road area. The senior judge was seriously injured, but his driver and eight security personnel escorting him suffered fatal wounds.
The bomb was reported to have been planted in a parked motorcycle and detonated by a remote control on the busy road in a high security zone of the city, yards from the Sindh High Court building and close to the Sindh Assembly, the Sindh Secretariat, and the headquarters of the provincial government.
Justice Baqar, a member of the Shia community, was said to be on the hit-list of religious militants, including the Lashkar-i-Jhangvi and Tehreek-i-Taliban Pakistan (TTP).
A spokesman for Tehreek-i-Taliban had claimed responsibility for the attack on the senior judge, claiming he was targeted due to his “anti-Taliban and anti-Mujahideen decisions”.
The jurist had served as the administrative judge of the anti-terrorism courts in Karachi and initially heard terrorism cases in this capacity.