Tuesday night, Aurora, a 10-year-old bear rescued in northern Ontario as an orphan, gave birth to three cubs at least six weeks early, the zoo said.
The bear killed one of the females and handlers rushed to take the remaining two near-furless cubs to the veterinary intensive unit for 24-hour care.
Thursday, the zoo announced the second female cub had died, the Toronto Sun reported.
A zoo official who didn't want to be identified told the Toronto Star Aurora had eaten the first female cub and badly mauled the second before handlers could intervene. The source said all of Aurora's first litter last year was stillborn and the bear has no experience at mothering.
Robert Buchanan, the president of conservation non-profit Polar Bear International, told the Star zoo handlers deserved high praise for their rescue efforts.
"How quickly they acted to spare them and save the others is just amazing," he said. "You just can't run in there and grab the litter; they are very dangerous animals."