The three victims died in Jinnah hospital where another 26 are being treated for consuming poisonous alcohol, said Dr. Seemi Jamali, chief of the hospital.
"The death toll could rise as five people are in critical conditions," she said.
The victims aged between 20-45 and included Muslim, Christians and Hindus. They were apparently getting the locally made cheaper liquor from bootleggers of the city.
Most of the dead belong to Landhi, Korangi, Sharafi Goth, Malir and Dawood Chorangi areas of Karachi.
Although alcohol consumption is banned in Pakistan, but non-Muslims are allowed to drink liquor by purchasing alcohol from government-controlled licensed liquor shops.
Last week, around 20 people had died in Sindh province's Hyderabad city after consuming toxic liquor.