Sharapova, ranked fifth in the world and seeded fifth at the talent-laden Dubai championships, won the Australian Open and last week's tournament in Qatar while running her 2008 record to 14-0. She was replaced in the Dubai draw by Akiko Morigami.
"I was really excited to come to Dubai this week and was very much looking forward to playing the Barclays Dubai Tennis Championships," Sharapova said in a statement.
"Unfortunately I have been battling a virus for several days and it's reached a point where I'm unable to compete. This is really disappointing to me, but I do intend to come back to Dubai next year and hopefully have a great tournament."