Er Shun, one of two pandas on loan to the zoo from China, gave birth earlier in the day to twins weighing just 187.7 and 115 grams.
Pandas are born blind and are only the size of a stick of butter. The cubs, which are 1/900th the size of their mother, are pink in color with short and sparse white fur.
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Zoo staff said Er Shun has demonstrated "excellent maternal instincts and began cleaning and cradling the first cub soon after its birth."
The two newborns, however, are very vulnerable and the coming days - which they will spend mostly in an incubator under observation by Canadian and Chinese panda experts - will be "critical to their survival."
"We are so proud to be contributing to the ongoing survival of this endangered species," zoo chief John Tracogna said in a statement.
Er Shun and Da Mao arrived in Toronto in 2013, and were welcomed by Prime Minister Stephen Harper and his wife. They will be moved to the Calgary zoo in 2018 for a five-year stay before returning to China.
The father of the cubs could be one of three pandas, including Da Mao, after Er Shun underwent two artificial insemination procedures in May, the zoo said.
Read: Hong Kong giant panda Jia Jia becomes oldest ever
Panda twins were born at Washington's Smithsonian National Zoo in August, although one died of pneumonia within a matter of days.
The surviving cub was named Bei Bei by US First Lady Michelle Obama and her Chinese counterpart, Peng Liyuan.
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