McCormack had earned a recall to the Scotland squad for the game at Pittodrie following Gordon Strachan's appointment as national team coach.
However, the forward will now sit out Strachan's first game after being sent home from the training camp as he is suffering from flu-like symptoms.
McCormack wrote on his Twitter account: "Gutted to be pulling out the Scotland squad ill... Now just rest and get fluids in me and be ready for wolves on Saturday!!"
The 26-year-old's last appearance for Scotland came at the start of this season when he scored in the 3-1 friendly win over Australia.
Strachan still has plenty of striking options at his disposal for the meeting with Estonia, with Kenny Miller, Steven Fletcher and Jordan Rhodes vying for a start.
Miller has often been deployed as a lone striker in recent years for Scotland, but the emergence of Rhodes and availability of Fletcher have given the national team greater depth up front.