A 73-year-old Saudi who suffered from chronic illnesses died in Riyadh and a compatriot diagnosed with the virus, aged 54, died in the port city of Jeddah, the health ministry said late Monday.
The ministry said it has registered 261 cases of infection across the kingdom since the discovery of the Middle East Respiratory Syndrome in September 2012.
The World Health Organisation said on April 17 that it has been informed of 243 laboratory-confirmed cases of infection with MERS worldwide, including 93 deaths.
Saudi Arabia on Monday dismissed its health minister, Abdullah al-Rabiah, without any explanation.
Rabiah last week visited hospitals in Jeddah to calm a public hit by panic over the spread of the virus among medical staff that triggered the temporary closure of a hospital emergency room.
MERS was initially concentrated in eastern Saudi Arabia but now affects other areas.
The virus is considered a deadlier but less-transmissible cousin of the SARS virus that erupted in Asia in 2003 and infected 8,273 people, nine percent of whom died.
Experts are still struggling to understand MERS, for which there is no known vaccine.
A recent study said the virus has been "extraordinarily common" in camels for at least 20 years, and it may have been passed directly from the animals to humans.