The man was the first person to die from hantavirus pulmonary syndrome contracted in the park, though two others were stricken in a more remote area in 2000 and 2010, officials said.
Testing by the Centers for Disease Control and the California Department of Public Health showed the virus was present in fecal matter from deer mice trapped in Curry Village, an historic, family friendly area of cabins.
"There's no way to tell for sure, but state health officials feel they may have contracted it here in Curry Village," park spokesman Scott Gediman said.
The names of the two people weren't released. The man was from Alameda County in the San Francisco Bay area. The woman from Southern California was expected to survive.
No other cases have been reported, but symptoms can show up one to six weeks after exposure. There is no specific treatment for the virus, and about one-third of people who contract it will die.
Hantavirus develops from breathing in dust particles contaminated with rodent droppings, urine or saliva. Early symptoms of hantavirus can include fever and muscle aches, chills, headaches, nausea, vomiting, diarrhea, abdominal pain and coughing.
Spokesman Ralph Montano of the California Department of Public Health said the agency was advising anyone with those symptoms to get medical attention and let doctors know if they were camping in Yosemite.
Montano said thousands of people visit Yosemite every month, so it would be impossible to track everyone who had set foot in Curry Village.
Curry Village is the most popular and economical lodging area in the park, a picturesque assemblage of rustic cabins at the base of the 3,000-foot promontory Glacier Point. Earlier this summer park officials placed some of the area off limits when a geologist's report revealed it is a rock fall hazard zone.
Both victims stayed at the park on overlapping days in June in canvas tent cabins located about 100 feet from each other, park officials said. Tent cabins are built on wooden platforms and are impossible to completely seal.
"It's a wilderness setting and the inspections have shown that the park concessionaire has done an excellent job at keeping them clean," Gediman said. "But there are rodents in the wilderness and some of them are infected and that's what happens."
There have been 60 cases in California and 587 nationally since hantavirus pulmonary syndrome was first identified in 1993. These two new cases bring to four the number of people stricken in California this year.
Most cases are in the eastern Sierra at higher elevations. The park's two previous cases were contracted in Tuolumne Meadows at 8,600 feet. Yosemite Valley is 4,000 feet.
Health officials say people should avoid contact with mice and other rodents. People should wear gloves and spray areas contaminated with rodent droppings and urine with a 10 percent bleach solution then wait 15 minutes before cleaning the area.
State health officials said their investigation showed that park concessionaire Delaware North Co. used good cleaning practices.
Company officials are telling visitors when they call to make reservations that the outbreak has occurred, said spokeswoman Lisa Cesaro. She said the company is working with the park service to come up with a plan to educate visitors about the potential danger.
"We are trying to see what ways we can educate visitors about hantavirus and the things they can do to keep themselves safe," she said. She said it's too early to tell whether the announcement has led to cancelled reservations at the hard-to-book village.
Starting next week, park officials will begin trapping and testing deer mice in Yosemite Valley.
"There's no way we're going to eliminate rodents, but we will continue to test and monitor them," Gediman said.
The Associated Press contributed to this report.