The 22-year-old Rahm was in a class of his own with two eagles and five birdies on the day as he finished on 24 under par overall.
Rahm joins 542nd-ranked American Daniel Im in a share of the lead as they head into the final day after an impressive run on the back nine, which saw him pick up four birdies.
Oner shot better at -18 and tied for second were Scotland's Richie Ramsay and England's Matthew Southgate, both thrilled with their week in Portstewart. Justin Rose, David Drysdale and Ryan Fox shared fourth.
Rahm was four clear when a query over his ball marking on the sixth green caused a concern on the 13th fairway.
The tournament formed part of the prestigious new Rolex Series of events, boasting a prize fund of £5.4m, and Rahm picked up £585,000 for his victory. McIlroy and Hideki Matsuyama give the Irish Open two of the top five players in the world ranking.
The double success increases the Scottish contingent in the 146th Open to seven, with Ramsay and Drysdale joining former victor Sandy Lyle and Paul Lawrie, as well as Russell Knox, Martin Laird and Connor Syme.
"Next year will be our fourth year as title sponsor of the Dubai Duty Free Irish Open hosted by the Rory Foundation, we very much enjoy working with our partners in the European Tour and indeed Rory McIlroy himself who has been a marvellous host for the last number of years". And the 28-year-old four-time major victor could not recover, his score of 73 taking him to a combined total of one over par at the halfway stage, ensuring the competition will head into the final two days without its marquee player. He will take a good deal of confidence into The Open at Birkdale - the course where he burst onto the scene as a teenage amateur in the championship of 1998.