Sindh Minister for Planning and Development Mir Hazar Khan Bijarani, 71, and his wife, former lawmaker Fariha Razzaq, were found lying in a pool of blood in the bedroom in their Defence Housing Authority residence, police said.
Both were shot dead at close range, they said.
A senior police official said the two bodies were found in the bedroom which was locked.
"A pistol has been found at the scene of the crime," Senior Superintendent of Police Raja Khatab of the Sindh Counter Terrorism department told the media.
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One member of the family of Bijarani said that the police had assured them the case would be looked at from every possible angle.
Sindh Chief Minister Murad Ali Shah, Home Minister Sohail Anwar Siyal, senior government and party officials reached Bijarani's house after the news of the minister's death broke.
Bijarani had served as a senator as well as a Member of National Assembly (MNA) and also held the portfolio of Sindh's Education Minister. He was elected in 2013 from PS-16 Jacobabad.
Pakistan People's Party (PPP) Chairman Bilawal Bhutto, whose party governs the southern Sindh province, asked the police to share all details with him.
Sindh Assembly Deputy Speaker Shehla Raza told the media that it was a very sad day and a great loss to the party.
"I am shocked and sad because one could never imagine such a thing happening," she said.