The feline -- whose species is the symbol of the Amazon -- was shot dead in the northern city of Manaus on Monday soon after it was photographed with the torch passing by. An attempt to use tranquilizer darts on it failed.
"It escaped and ran off as it was being moved from one area to another in the zoo," said Colonel Luiz Gustavo Evelyn, whose unit is deployed in the region.
He explained that, once located, the jaguar was hit by four tranquilizer darts. But they did not slow it down and it turned on a veterinarian, forcing the soldiers to use bullets.
"To protect the handler, it was sacrificed," Evelyn said.
The animal, a 17-year-old female named Juma, had been raised since it was a cub and was kept in the military-run zoo in the Amazon with half a dozen siblings.
Just before its escape, it and another jaguar had been exhibited as the Olympic torch crossing Brazil passed through the zoo on its way to Rio de Janeiro, which is hosting the Games due to start August 5.
"Unfortunately, this occurred the day of the torch's passage," Evelyn said. "The animal participated in the event because the torch went through the zoo."
He added that Juma was not a wild animal, having been raised in captivity, and called its death "very sad."
The military has opened an investigation into the incident.
The jaguar is the biggest feline in the Americas. It can weigh up to 135 kilograms (300 pounds) and is in danger of extinction.
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