McIlroy has never won his home open and missed the cut on the last three stagings, but inspired play insured he would land the trophy at an event he hosts for his foundation.
Scotsman Russell Knox had taken a one-shot lead from longtime pacesetter McIlroy with three holes to play until the four-time major winner unleashed his magic.
Sensational approach shots to the par-five 16th and 18th at the K Club secured him a birdie and closing eagle.
He also lipped out a birdie putt on the 17th as Knox faded to three shots behind at the end, tied second with Welshman Bradley Dredge.
As he approached the final green, with victory in the bag, McIlroy was visibly moved before tapping in the shortest of eagle putts.
"I don't really get emotional when I win, but I was holding back the tears there. To play like that and finish like that, with all of my friends and family watching was just so special," the Northern Ireland star admitted.
A closing 69, all his gains against par made in the closing three holes, left the world number three on 12-under 276. He donated the euro 666,000 ($747,000) first prize to his foundation.
It was his first victory as a professional on Irish soil and his first since claiming last November's European Tour season-ending World Tour Championship in Dubai.
Another player in tears at the finish was Englishman Matthew Southgate, who has battled testicular cancer to earn his European Tour card and took a fine fourth on eight under.
Germany's Martin Kaymer powered through the field on the closing day with a 65 to finish in a tie for fifth, but Masters champion Danny Willett, in contention overnight, slumped to a five-over 77.
McIlroy, who has had six top-10 finishes this season ahead of his victory, will now target the second major of the season, the U.S. Open at Oakmont, where he will continue his battles with Jason Day and Jordan Spieth, the two players ranked ahead of him.