The geriatric rhino had arthritis and other ailments and was being treated for a bacterial infection linked to an abscess in her hip.
Nola had surgery on Nov. 13 to drain the abscess but her health began to deteriorate about a week ago.
The 4,000-pound Nola had been placed under constant veterinary watch as her appetite and activity levels declined.
She worsened over the past 24 hours and vets decided they had to euthanize her, according to the zoo in Escondido.
"Nola was an iconic animal, not only at the San Diego Zoo Safari Park, but worldwide," the park statement said. Her gentle disposition and affinity for having her back scratched made her a favorite of zoo staff.
Nola was a 41-year-old female who was born wild in Sudan and captured when she was about 2 years old, according to the San Diego Union Tribune. She arrived at the zoo in 1989. The hope was that Nola would mate with Angalifu, who was at the park. Although the pair mated, there was never a pregnancy.
The remaining three northern white rhinos, all elderly, are in Ol Pejeta Conservancy, a closely guarded preserve in Kenya.
The subspecies has been decimated by poachers, who kill the rhinos for their horns. The horns are in high demand in parts of Asia where some people claim they have medicinal properties for treating everything from hangovers to cancer.
In an effort to preserve the species, the San Diego zoo took possession earlier this month of six female southern white rhinos from South Africa.
The zoo has northern white rhino cells stored at the Frozen Zoo that could be used to create healthy future generations.
Zoo researchers are working on developing northern white rhino embryos to be implanted in the six new arrivals, who will serve as surrogate mothers.
Researchers have said they hope a northern white rhino calf could be born from a San Diego surrogate mother within 10 to 15 years.
Scientists remain unsure whether northern and southern white rhinos are two distinct species or subspecies of each other.
Studies are under way to determine if southern whites, of which fewer than 20,000 are estimated to remain in the wild, are genetically similar enough to serve as maternal surrogates for implanted embryos that would be developed from northern white rhino DNA, zoo spokeswoman Christina Simmons said.
Wildlife experts say southern white rhinos are killed by poachers at the rate of three a day.
Al Jazeera with wire services