Hussain was booked under section 295-C of the Pakistan Penal Code, the harsh blasphemy law.
A district and sessions court acquitted him last month for lack of evidence.
On Friday, Hussain was at his shop when two armed men came and fired at him. He was killed instantly. The two gunmen later surrendered to police.
They were identified as Sheikh Zeeshan and Awais Ahmed, both residents Hussain's neighbourhood.
The men told police that they had killed a "blasphemer" and had no regrets over their action.
Hussain's family held a demonstration and demanded that the two men be punished.