ABU DHABI, January 18, 2014 (AFP) - McIlroy finished his third round with a bogey-free 68, but that turned into a 70 after a video and on-spot review.
He was found in breach of Rule 25-1 for not taking a full relief from a spectator's crossing on the second hole of the Abu Dhabi Golf Club.
Last year, Tiger Woods was penalized two shots for taking a wrong drop in the same tournament, thus missing the cut by one, and in 2011, Padraig Harrington was disqualified for moving the ball.
McIlroy, who would have finished one shot behind the leader Craig Lee, finished on nine-under par 207.
Lee shot a 69 and was on top of the leaderboard at 204.
Two shots behind were Phil Mickelson, who stormed into contention with a stunning round of nine-under par 63, and India's Gaganjeet Bhullar, playing his first season as a full member of the European Tour, who shot a bogey-free 66.
McIlroy later explained: "I hit my second shot on the second hole just into the left rough, but it was in the spectator crosswalk, so I took a drop, which obviously you're allowed to do out of it.
"I didn't notice it but my left foot was still on the white line as I played the shot and need to take full relief. I actually dropped it in a really bad lie, so actually had I known, I would have taken a better drop.
"I guess I was just so much into the shot that I didn't even realize. It was unfortunate, but that's the rules of this game. I don't feel like I gained any sort of advantage by my foot being on a bit of white paint."
Dave Renwick, the caddie of his playing partner Ricardo Gonzalez, noticed it and asked McIlroy on the 18th hole not to sign his card and asked for clarification.
McIlroy said he was going to hit the gym to take out his frustration and come out recharged Sunday morning.
"I guess I just have to try to make up those shots as early as possible tomorrow, try to get off to a fast start.
"I felt like I hung in there well and had a lot of opportunities on the back nine that I didn't take. It was all sort of in vain, so I'll need to go out there and get off to a good one tomorrow," added McIlroy.
Mickelson, who could not make a birdie in his first 21 holes in the tournament, made nine birdies and an eagle Saturday for a 63, just one shot short of Henrik Stenson's course record of 62.
After carding his final birdie of the day on the 18th from a horrible lie, Mickelson said: "I got a little tired those last four or five holes, and I could tell that it was early in the season and I wasn't quite as sharp as I was early on. So that's something that I'll be able to work on.
"I made a few lazy swings in the end, but I hit a lot of good shots, the irons felt pretty good, and earlier in the day I was putting the ball in play and it felt good."
Lee, who made two bogeys in his 69, is looking for his first win on the European Tour, said: "I am delighted. It was obviously a strong pack behind me.
"You can tell from the leaderboard that there are a lot of good players starting to make a charge; so I'm delighted to still be the one in the lead."
Collated third-round scores in the $2.7million Abu Dhabi HSBC Golf Championship on Saturday at the par-72 Abu Dhabi Golf Club:
204 - Craig Lee (SCO) 68-67-69
206 - Phil Mickelson (USA) 73-70-63, Gaganjeet Bhullar (IND) 72-68-66
207 - Pablo Larrazabal (ESP) 69-70-68, Rory McIlroy (NIR) 70-67-70
208 - Miguel Angel Jimenez (ESP) 73-68-67, Thongchai Jaidee (THA) 70-70-68, Matthew Baldwin (ENG) 67-72-69, Michael Hoey (NIR) 69-71-68, Rafael Cabrera-Bello (ESP) 67-68-73
209 - Peter Hanson (SWE) 70-70-69, Thomas Bjorn (DEN) 70-67-72
210 - Jose Filipe-Lima (POR) 68-75-67, Martin Kaymer (GER) 70-71-69, Otto Hennie (RSA) 70-71-69, Tyrell Hatton (ENG) 69-71-70, George Coetzee (RSA) 68-70-72, Joost Luiten (NED) 68-70-72, Tommy Fleetwood (ENG) 73-65-72
211 - Stephen Gallacher (SCO) 70-73-68, Eddie Pepperel (ENG) 70-72-69, Marc Warren (SCO) 68-73-70, Alvaro Quiros (ESP) 71-70-70, Ricardo Gonzalez (ARG) 71-66-74
212 - Andy Sullivan (ENG) 73-70-69, Alexander Levy (FRA) 74-69-69, Thomas Aiken (RSA) 70-73-69, Romain Wattel (FRA) 67-75-70, Edoardo Molinari (ITA) 70-71-71, Robert Karlsson (SWE) 73-67-72, Paul McGinley (IRE) 68-72-72, Marcel Siem (GER) 69-70-73, Danny Willett (ENG) 73-63-76
213 - Branden Grace (RSA) 73-70-70, Raphael Jacquelin (FRA) 71-72-70, Tom Lewis (ENG) 71-70-72, Rapahael Jacquelin (FRA) 71-72-70, Ricardo Santos (POR) 70-72-71, Wade Ormsby (AUS) 69-73-71
214 - Sergio Garcia (ESP) 76-68-70, Matteo Mannasero (ITA) 71-73-70, Emiliano Grillo (ARG) 72-72-70, Luke Donald (ENG) 70-73-71, Johan Carlsson (SWE) 73-70-71, Maximilian Kieffer (GER) 71-71-72, Oliver Fisher (ENG) 69-72-73
215 - Thorbjorn Olesen (DEN) 74-70-71, Darren Clarke (NIR) 74-69-72, Seve Benson (ENG) 73-70-72, Brandon Stone (RSA) 71-71-73, Colin Montgomerie (SCO) 73-68-74, Dawie van der Walt (RSA) 68-73-74, Darren Fichardt (RSA) 70-70-75
216 - Chris Wood (ENG) 71-73-72, David Howell (ENG) 73-71-72, Eduardo de la Riva (ESP) 70-74-72, Paul Casey (ENG) 72-71-73, Jamie Donaldson (WAL) 73-70-73, Nacho Elvira (ESP) 72-70-74, Alejandro Canizares (ESP) 71-69-76
217 - Peter Whiteford (SCO) 74-70-73, Jose Maria Olazabal (ESP) 74-70-73, Jorge Campillo (ESP) 72-72-73, Julian Quesne (FRA) 71-72-74, Damien McGrane (IRE) 70-72-75, Seve Webster (ENG) 69-73-75, Jin Jeong (KOR) 70-71-76
218 - Jeev Milkha Singh (IND) 69-75-74, Paul Waring (ENG) 73-71-74, Shiv Kapur (IND) 71-72-75
219 - Richard Bland (ENG) 71-73-75, Gareth Maybin (NIR) 70-73-76, Magnus A Carlsson (SWE) 71-71-77