The Northern Irishman played through the pain in losing a play-off to Graeme Storm at the BMW SA Open on Sunday, having said on Friday morning he had considered pulling out of the event due to the problem.
He underwent a scan on Monday morning and has been diagnosed with a stress fracture to a rib.
McIlroy said in a statement: “It’s bitterly disappointing to have to withdraw from the Abu Dhabi HSBC Championship. I think everyone knows how much I love playing this tournament, which is one of the best on the European Tour thanks to the incredible support of HSBC and the Abu Dhabi Sports Council.
“To be forced to miss this week through injury is really quite annoying to be perfectly honest, but I am sure the tournament will be a huge success and I hope everyone involved has a great week.
“In situations like this you simply have to listen to the experts and the team I have consulted have all advised me to rest until my rib has fully recovered.”
McIlroy had initially cited the problem as suspected fatigue after an off-season that has seen him hit a lot of balls in practice trying to decide on new equipment after former supplier Nike decided to stop producing clubs last year.
He played in Johannesburg with his back taped up while taking anti-inflammatories.
American stars Dustin Johnson and Rickie Fowler – the defending champion – are due to play in Abu Dhabi, where McIlroy has finished outside the top three only three times in nine appearances.