Shuwail al-Amri was found guilty of killing Mohammed al-Amri, an apparent relative, by deliberately running him over with a car after a dispute, the ministry said in a statement published by SPA state news agency.
The execution took place in the southwestern region of al-Baha.
In another statement, the ministry said Hasan Sharahili, a Saudi, was executed after a court found him guilty of shooting dead his compatriot Mohammed Abdullah Musbeh al-Amri in the southwestern city of Jizan.
Their beheadings bring to 49 the number of people executed in the ultra-conservative kingdom this year.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia's strict version of sharia, or Islamic law.