The 4-year-old koala had developed the cysts associated with urogenital chlamydiosis, which affects more than 50 percent of Australia's koala population.
During surgery, the disease was found to be so advanced that it was inoperable and Sam was euthanized, said Peita Elkhorne of TressCox law firm, which represents the shelter where the koala had lived since the February fires.
"It was so severe that there was no possible way to be able to manage her pain," Elkhorne said in a statement. "All of those who have been involved with Sam are devastated with this loss."
John Butler, the veterinarian who was conducting the operation, said Sam was too scarred inside to carry out the surgery.
"She was going to be left in pain in the state she was in," Butler told reporters. "We had no hope of helping her any further."
As fires raged, Sam was gingerly making her way on scorched paws past a fire patrol north of Melbourne when one of the firefighters spotted her. The volunteer firefighter, David Tree, was photographed holding a bottle of water to her lips, an image that resonated around the world.
Tree was in tears Thursday as he spoke to reporters about Sam's death.
"It means something to everyone," he said. "The focus was never meant to be ... on a firefighter. It's simply about our wildlife and just how precious it is."
Prime Minister Kevin Rudd said the photograph and video made Sam a symbol of hope for Australia.
"I think that gave people of the world a great sense that this country, Australia, could come through those fires, as we have," Rudd said. "And Sam the koala was part of the symbolism of that. It's tragic that Sam the koala is no longer with us."
Sam suffered second- and third-degree burns to her paws and had been recuperating at the Southern Ash Wildlife Shelter. Officials there had said she would be returned to the wild within months after she was completely healed.
It was not known whether Sam had the infection before the fire. The disease, one of the main killers of the koala, is brought on by stress.
Deborah Tabart, CEO of the Australian Koala Foundation, said she was saddened by Sam's death but noted that thousands of other koalas die every year of the disease and are not lamented nor cared for by the government.
"Sam's just the tip of the iceberg," Tabart said. "Sam's doing her wild cousins a huge favor by this international interest. Our koalas are in serious trouble across the country."
Sam was found in early February, when record temperatures, high winds and forests dried by years of drought set off infernos that swept a vast area of Victoria state, killing more than 170 people and destroying thousands of homes.
