The shooting came just three days after a gunman, identified as a wanted jihadist, killed nine people in an attack on a church south of the capital.
An assailant rode up in the back of a motorcycle taxi and opened fire on the liquor store in Cairo's twin city Giza at around 1:30 am (local time), when the streets were still bustling with New Year revellers, the sources said.
The store's Coptic owner survived but two of his friends who were celebrating with him were killed.
Alcohol consumption is forbidden by Islam and liquor stores, most of which are run by Copts, have come under attack in the past by hardline Muslims who believe they should be banned.
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On January 2 last year, a Muslim slit the throat of a Coptic liquor store owner in the Mediterranean coastal city of Alexandria.
The assailant was sentenced to death after telling the court that he would kill all alcohol sellers if he could.
Egypt's Coptic Christians make up about 10 per cent of the country's 93 million people, and are the largest religious minority in the region.