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.
No timetable has been given for his return, but the European Tour announced he would miss this week’s event in Abu Dhabi.
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, who is the defending champion, are due to play in Abu Dhabi, where McIlroy has finished outside the top three only three times in nine appearances. McIlroy’s withdrawal has elevated Duncan Stewart, who’d been sitting as first reserve, into the field, joining David Drysdale, Richie Ramsay, Marc Warren, Scott Jamieson, Paul Lawrie and Stephen Gallacher.
“Delighted to get in to @ADGolfChamps,” wrote Stewart on Twitter. “The course looks fantastic and can’t wait to get started on Thursday. Hope @McIlroyRory is back playing ASAP.”
Scotland, represented by Greig Hutcheon, Graham Fox and Greg McBain, set out in Turkey today bidding to go one better in the PGAs of Europe International Team Championship.
Fox is the sole survivor from 12 months ago, when Gareth Wright and David Orr were the other members of a team pipped for the title by France at Gloria Golf Club.
Fox won the individual event on that occasion with a 14-under-par 274 total.
McBain is making his return to the event, having played with Fox and Orr two years ago, when the Scots also finished second.
“I couldn’t really pick better team-mates as they are both great players with a lot of experience,” said the Newmachar PGA pro.
“I’ll learn a lot from them this week. I’m looking forward to competing again, and obviously expectations are high with past results.
“It’s a great set up here at Gloria, so we will see what happens.”
Hutcheon, who is attached to Paul Lawrie Golf Centre Inchmarlo, will be hoping to take up where he left off in his last competitive outing.
The Tartan Tour No 1 finished joint-third in the PGA Play-Offs at Saunton, where he also beat Irishman Damien McGrane in a play-off to secure a PGA Cup spot later this year.
Four players will qualify for The 146th Open at Royal Birkdale when The Open Qualifying Series arrives in Singapore this week.
The SMBC Singapore Open, hosted by Sentosa Golf Club and jointly sanctioned between the Asian Tour and the Japan Golf Tour, is part of the Series for the first time in 2017.
Two-time Open champion Ernie Els, Adam Scott, Sergio Garcia and the defending champion, Younghan Song, are all scheduled to play in the event.
Four players who finish in the top 12 and ties, who are not already exempt, will earn places in the field at Royal Birkdale next July
Seven Scots, including Challenge Tour card holder David Law, are playing in the Pro Golf Tour’s Red Sea Egyptian Classic, which starts today.
The double Scottish Amateur champion is joined in the field at Sokhna Golf Club by Ross Cameron, Zander Culverwell, Chris Robb, Kevin Duncan, Philip McLean and Sam Kiloh.
The 54-hole event carries a €30,000 prize fund.
Masters champion Danny Willett has become a global brand ambassador for Descente, a leading luxury sportswear compane.
The world No 11 has signed a long-term golf and athletic apparel sponsorship deal to showcase the trend-setting brand’s golf clothing collection.
He will wear Descente for the first time at this week’s Abu Dhabi HSBC Golf Championship.