There were birdies to be had but even those taking advantage could only get to three under for their rounds at best and with heavier rain and wind gusting up to 35mph forecasted, scores were only likely to get higher.
Lowry will be aided by what is essentially a home crowd at Royal Portrush.
Italian Francesco Molinari finished his year as Open champion with a fine 5-under-par 66 to be 3-under-par for the tournament.
Resuming on four under, Lowry birdied four of the opening five holes and picked up another two shots on eight and 10 to move to 10 under.
England's Danny Willett was on four under for his round after 11 holes and five under for the tournament.
After hitting his final approach shot he held his arms aloft in celebration and hugged his caddie, assured finally that there would be no late disaster. The loudest cheer of a raucous week was for a tap-in par that made Lowry a major champion.
Tony Finau was also delighted after finishing third behind Shane Lowry and Tommy Fleetwood with a final-round 71 to finish on seven under. He closed with a 74. He started the day at 9-under and 7 shots behind Lowry.
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McIlroy didn't know what to expect after Thursday's 79, whether anyone would still turn up for him on the first tee. The other Ulstersman, Portrush native Graeme McDowell, basked in the loudest cheers he has heard this side of the Ryder Cup when he walked up the 18th green on Sunday.
Shane Lowry surely understands, too, though his memories are more bittersweet.
However, it looks set to be a shootout between those two for a first ever major with the awful conditions hampering the chasing pack's chance to post a challenging score.
Lowry knew questions regarding that US Open would follow his round and he said that he hopes he's better equipped to deal with the pressure this time around.
"I didn't feel great out there".
The Irishman said afterwards: "It was one of the most incredible days of my life".
"I'm just projecting Shane is going to have a decent finish here, he's got a great short game, that will stand him in good stead on a tough weather day, he's Irish". He almost gave away his last major just two months ago after leading by seven shots going into the final round of the PGA Championship. The wind was picking up and it was relentless for so much of the day. Then on the final nine holes, things started to unravel for Lowry a bit as he bogeyed the 14th and 18th holes after collecting a birdie on the 10th.
Everyone except Fleetwood fell back.
Holmes teed off in third place, six strokes behind Lowry, yet it was to prove anything but elementary for the man from Kentucky. He hit his first tee shot out-of-bounds.