The man, Mazyad al-Obeidi, shot dead a Saudi national following an argument, the ministry said in a statement carried by the official SPA news agency.
His execution in the capital brings to 68 the number of people executed in Saudi Arabia so far this year, according to an AFP count.
In 2012, the conservative Muslim kingdom carried out 76 executions, according to a tally based on official figures. Human Rights Watch has put the number at 69.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under the oil-rich Gulf state's strict version of sharia, or Islamic law.
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