Yussef al-Nafii, executed in the western city of Taif, had been convicted of shooting fellow Saudi Salman al-Rabii dead after a dispute, the ministry said in a statement carried by the official SPA news agency.
In the other case, Abdessalam al-Ruili was beheaded in Arar in the north for stabbing to death compatriot Abdessalam al-Anzi following an altercation, the ministry said.
The beheadings raise to 28 the number of executions announced in Saudi Arabia so far this year, according to an AFP tally.
Last year, there were 78 executions in Saudi Arabia and the UN High Commissioner for Human Rights denounced a "sharp increase in the use of capital punishment".
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under the kingdom's strict version of Islamic sharia law.