A 75-year-old woman, who had suffered chronic illnesses, died in the western city of Medina, while a man, 83, who also had chronic diseases, died in the capital, the ministry website said.
The ministry also registered three new cases, bringing to 107 the total number of infections in Saudi Arabia, the country worst hit by the virus.
The World Health Organisation said on September 7 that it has been informed of 114 cases of MERS infection worldwide, among them 54 fatalities.
Experts are struggling to understand MERS -- Middle East Respiratory Syndrome -- for which there is still no vaccine.
It is considered a cousin of the SARS virus that erupted in Asia in 2003 and infected 8,273 people, nine percent of whom died.
Like SARS, MERS is thought to have jumped from animals to humans, and it shares the former's flu-like symptoms -- but differs by also causing kidney failure.
The MERS problem persists in Saudi Arabia, which is gearing up to host around two million Muslims in October for the annual hajj pilgrimage to Mecca.
Authorities have urged the elderly and chronically ill to avoid the hajj this year and have cut back on the numbers of people they will allow to perform the pilgrimage.