Awadha Ahmed Salem was convicted of raping and killing the unidentified women and burning the corpse of one of them with acid, the ministry said in a statement carried by SPA state news agency.
His execution in the western Medina region brings to 20 the number of death sentences carried out this year in the ultra-conservative kingdom.
Saudi Arabia beheaded 78 people in 2013, according to an AFP count.
Last year, the UN High Commission for Human Rights denounced a "sharp increase in the use of capital punishment" there since 2011.
In 2012, the number of executions dipped slightly to 79, among them 27 foreigners.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia's strict version of Islamic sharia law.