The Pinta Island tortoise will be on display on Santa Cruz Island for future generations to see, Environment Minister Marcela Aguinaga said.
A necropsy determined Lonesome George, estimated at 100 years old, died of old age, she said.
As the only known living example of his subspecies, Chelonoidis nigra abingdoni, Lonesome George was considered the rarest creature in the world.
Efforts to get the Pinta Island tortoise to reproduce with females from a similar subspecies on the Galapagos Islands all met with failure, the BBC reported.
Lonesome George had become a symbol of the Galapagos. An estimated 180,000 people annually visit the islands where Charles Darwin began to formulate his theories on evolution.