Toronto recalled 20-year-old Antoine Bibeau on Saturday afternoon with Bernier sick, but interim coach Peter Horachek went back to Reimer to face the Edmonton Oilers.
Bernier was originally slated to start after Reimer played in Friday night's loss at the New Jersey Devils and took part in the optional morning skate at Air Canada Centre.
Bibeau was recalled from the AHL's Toronto Marlies under emergency conditions with defenceman Dion Phaneuf put on injured reserve to make room on the roster.
Earlier on Saturday, the Leafs recalled defenceman Petter Granberg because of an injury on the blue-line that Horachek did not want to reveal. Cody Franson (lower-body injury) looked to be the odd-man out after warm-ups but was in the lineup with Granberg scratched.
Winger David Clarkson was made a surprise healthy scratch, his first time out of the lineup in that fashion since signing with the Leafs in the summer of 2013.
Clarkson, who missed 10 games with suspension and nine with injury last year, has 10 goals and five assists in 53 games this season.