The winner of last month's Portugal Masters was taken to a Dubai hospital earlier this week after experiencing severe headaches and vomiting.
"I am gutted to have been forced to withdraw," Lowry said in a statement. "It is such a big week and a great event but given the way I feel right now there is no way I could have played golf today.
"I honestly couldn't even stand up on the tee, never mind play 18 holes."
World number 57 Lowry said he picked up the virus at the start of the week and became "very sick and dehydrated".
"I went to hospital yesterday where they put me on a drip," said the 25-year-old Dubliner, who was an amateur when he captured his first tour title at the 2009 Irish Open.
"That helped but when I came off the drip and left hospital I became sick again and haven't been able to keep rehydrating to keep the recovery going overnight. With the best will in the world there is no way I would have been able to compete."
There are now 56 players left in the $8 million tournament following the earlier withdrawals of Dane Thomas Bjorn, South African Retief Goosen and Briton Ross Fisher.