The four-time major winner had seen his one-shot overnight lead evaporate on a day where 40 mph winds made scoring difficult at the Renaissance Club.
But having missed from eight feet for birdie on the par-five 16th, the Northern Irishman made no such mistake from closer range on the par-three 17th to join Scotland's Robert MacIntyre on 14 under.
McIlroy then played a stunning approach shot on the 18th before a successful 10-foot putt snatched victory from MacIntyre.
"I'm really proud," said McIlroy, who will return next week to the scene of his only British Open triumph at Hoylake in 2014 -- the last of his four major titles.
"That was such a tough day, especially the back nine. To play that in four under par to win the tournament I'm really proud of how I stuck in there, hit some amazing shots down the stretch and was able to finish it off."
Victory in the £7 million Scottish Open gave McIlroy his second Rolex Series title of the year.
'Shot of confidence'
"It feels incredible," he added. "It's been a sort of long six months I feel since I won in Dubai. I've given myself tons of chances and hopefully this win sort of breaks the seal for me, especially going in to next week as well."
He added: "It's a great shot of confidence and helps having something fresh in my memory. If I hopefully find myself in a similar position next week where I have a chance to win with nine holes to go, I can certainly draw on what I did here.
"I haven't seen Hoylake since 2014 so I'll get out on the course on Monday and try to figure it out and make sure I'm ready."
MacIntyre had a lucky break when a wild drive on the 18th managed to find the spectator walkway. But he made the most of his good fortune with a superb approach shot that landed within four feet of the hole.
The left-hander started the final round five shots behind McIlroy but followed up on his promise to enjoy " "absolutely brutal" weather, with birdies on the third and sixth holes followed by an even better eagle on the par-five 10th.
His birdie on the 14th gave MacIntyre the outright lead for the first time and he doubled his advantage on the next.
McIlroy remained in contention with a birdie on the 11th and a par save on the 12th, where the world number three thought he had missed his putt only for the ball to catch the edge of the hole and drop in.
Then, after MacIntyre bogeyed the par-five 16th, McIlroy holed from almost 40 feet on the 14th to share the lead.
MacIntyre's outstanding birdie on the 18th completed an excellent 64 and edged him back in front again.
But he was denied what would have been the biggest win of his professional career by McIlroy's fine finish over the last two holes.
"I've grown up watching Scottish Opens and my dream was always to win one," said MacIntyre.
"I thought today might have been the day, but it wasn't to be. I'm absolutely gutted just now, but I take my hat off to Rory. What a finish."
