McIlroy went into the day having suffered a two stroke penalty yesterday for an incorrect drop at the second hole.
The penalty came back to haunt him, as he finished on 13 under par, one shot off the winner Pablo Larrazabal.
Michael Hoey finished in a tie for tenth place on 7 under, with Paul McGinley one shot further back in a tie for 19th.
Darren Clarke finished on level par, Gareth Maybin was on 4 over and Damien McGrane on 5 over.
