Three men, including the two Hindus, were at the 'Super Wine shop' in Gulshan-e-Iqbal area here yesterday when the gunmen opened fire, killing them on the spot.
The owner of the shop, Taru Mal, escaped unhurt.
"Apparently Taru Mal had been receiving calls from a Dubai number for extortion money and he refused to pay," Senior police official Rao Anwar said.
He said security had been increased at the two wine shops Mal owned after he got the threatening call following a shootout warning him he would be the next target.
In Pakistan, where alcohol consumption is banned for Muslims, the government issues licenses for wine shops run by its excise department where only non-Muslims and foreigners can purchase liquor.
Most of these wine shops are run by Christians or Hindus in Karachi.