Emergency services found the girl unconscious after being called to a residence in Thurso, Que., on Wednesday.
Her 25-year-old father was arrested hours later and charged with aggravated assault during a court appearance Thursday.
The Crown opposed the man's release and he will remain behind bars at least until the case resumes Monday.
A police officer confirmed on Thursday the baby had symptoms associated with shaken baby syndrome. She died Friday night.
Police say an autopsy will be conducted early next week and may lead to more charges being laid.