The ministry said five more people were infected with the Middle East Respiratory Syndrome in the western city, including two foreign medics aged 54.
The latest deaths of a 64-year-old and 44-year-old, whose nationalities were undisclosed, bring to 76 the overall number of people to have died of MERS in Saudi Arabia, from a total of 231 infections.
Panic over the spread of MERS among medical staff in Jeddah this month forced the temporary closure of a hospital emergency room, prompting Health Minister Abdullah al-Rabiah to visit the facility in a bid to calm the public.
On Wednesday, at least four doctors at the King Fahd hospital reportedly resigned after refusing to treat MERS patients, apparently out of fear of infection.
MERS was initially concentrated in eastern Saudi Arabia but it now affects other areas.
The World Health Organisation said Thursday it had been told of 243 laboratory-confirmed cases of MERS infections worldwide, of which 93 have proved fatal.
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 may have been passed directly from the animals to humans.