Gezi, who had already given birth earlier this year, collapsed and suffered cardiac and respiratory arrest at about 12:15 p.m.
The necropsy showed Gezi had enlarged lymph nodes, inflammation within her gastrointestinal tract and more than 100 "suspicious black masses" throughout her body, zoo officials said. They did not elaborate on what the masses might be.
Gezi's cause of death will not be determined until after a histopathology exam is completed.
Zookeepers told veterinary staff on Sunday that Gezi had a decreased appetite. The giraffe was given antibiotics and fluids, and blood tests were taken, which came back normal, zoo officials said.
Veterinarians performed a physical exam, re-checked her blood and gave Gezi additional intravenous fluids and electrolytes Tuesday morning prior to her death, zoo officials reported.
Gezi, who came to the zoo at age 2 in 2001, gave birth to offspring Terrance on May 18, 2006 and Barbro on Feb. 25.
The average life span of a female giraffe held in captivity is about 25 years.
With the loss of Gezi, the San Francisco Zoo is left with one adult male and two adult females giraffes, and two calves, one male and one female.