Corporal Shaalan bin Nasser al-Qahtani and Lance Corporal Fahd bin Hassan al-Sebeyi were convicted of attacking an expatriate and raping his niece at a checkpoint they were manning in the capital, the ministry said in a statement carried by SPA state news agency.
They had stopped them late in the night, beat the man up and locked him in a police car and then raped the woman, it added, without revealing the age or nationality of the victims.
The two men were arrested shortly after the victims reported them at the nearest police station, it said.
Their executions bring to 11 the number of beheadings announced by the Saudi authorities since the beginning of the year. A total of 102 people were executed last year.
Death penalty will be executed for rape, murder, apostasy, armed robbery and drug trafficking in Saudi Arabia. Execution will take place in public places usually.