No one was injured in the incident that occurred in Light House area of Karachi.
The armed men had sent a note demanding money to the shop. Having paid Rs 500,000 in extortion during the Islamic holy month of Ramzan, Hussain's nephew refused to pay money this time, Express News channel reported.
Police said the extortionists who sent the note had been identified.
The President is a businessman from Karachi and a close aide of Prime Minister Nawaz Sharif.