The Austrian was due to meet Frenchman Gael Monfils in the semi-final following a straight-sets win over promising youngster Stefanos Tsitsipas.
Guido Pella or Andey Rublev will now meet Monfils in the final in Doha.
Thiem had not dropped a set in Doha but had coughed repeatedly during a press conference on Thursday, raising concerns about his condition.
“I am in bed with fever and there is almost no chance of a recovery until tonight,” Thiem wrote on Facebook.
“Of course I am disappointed, but nevertheless I had a solid start into the new season.
“Now I am focusing on Melbourne and being fit and prepared for the first Grand Slam of the year,”