Sabri, 45, and an associate were travelling in a car in Karachi's congested Liquatabad 10 area in June when two motorcycle-borne gunmen fired at their vehicle, killing them.
The victims were apparently heading for the studio of a private TV channel when they were attacked.
"The Counter-Terrorism Department headed by Raja Umar Khattab made a major breakthrough and arrested two people from Liaquatabad called Ishaq alias Bobby and Asim alias Capri. Their weapons were also recovered," he said.
"Asim alias Capri was Sabri's neighbour. We have not found any motive (behind the murder) as yet, but it seems sectarian to us because Sabri used to frequent majalis (religious congregation of minority Shia community)," the Dawn quoted him as saying.
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Shah said there was 'conclusive proof' that the two were part of a gang involved in nine 'major incidents'.
"After a probe and forensic investigation, we found proof of (their) involvement in 28 cases," he said.
"We will try to follow the lead through the arrested ones and apprehend rest of the gang," he added.
Amjad Sabri was the son of renowned Qawwal Ghulam Farid Sabri whose family is famous in the subcontinent for their contribution to this sufi art and mystic poetry.
Sabri was one of Pakistan's finest qawwals, known for his soul-stirring renditions of mystic poetry.
Some of the most memorable and famous qawwalis of the Sabris were 'Bhar Do Jholi Meri', 'Tajdar-i-Haram' and 'Mera Koi Nahin Hai Teray Siwa'.
Sabri, who travelled widely to Europe and the US for his concerts, was known as the "rockstar" of Qawali due to his modern style of rendition.
The LeJ has roots in Punjab province and has a history of carrying out sectarian attacks in Balochistan, particularly against the minority Shias.
The group recently claimed that it killed 61 people, mostly young cadets, during an attack on a police training centre in Quetta, the capital of the restive Balochistan province, in one of the deadliest terror attacks in Pakistan.