The world number two from Northern Ireland made a double bogey at the fourth and a bogey at the sixth, but responded with four birdies in the next seven holes and hung on after woeful late tee shots to win a second green jacket and a record top prize of $4.5 million.
McIlroy joined Tiger Woods, Jack Nicklaus and Nick Faldo as the only back-to-back winners in Masters history, firing a final round one-under-par 71 to finish on 12-under-par 276 and defeat top-ranked Scottie Scheffler by one stroke.
A year after winning his first Masters to complete a career Grand Slam and snap a 10-year major win drought, McIlroy pulled off a wire-to-wire triumph.
"I just can't believe I waited 17 years to get one green jacket and you know I get two in a row. It's just sort of the way," McIlroy said.
"I think all of my perseverance at this golf tournament over the years has really started to pay off."
Augusta National chairman Fred Ridley placed the green jacket on McIlroy, a role usually reserved for the prior year's Masters winner.
McIlroy seized a 36-hole Masters record six-stroke lead only to play the weekend at level par.
"It was a tough weekend. I did the bulk of my work on Thursday and Friday," McIlroy said. "But just so, so happy to hang in there and get the job done."
McIlroy, third-from last in driving accuracy for the week, saved par at 15 from trees but sent his tee shot at the 18th over right trees to a spot near the adjacent 10th fairway.
With a victory at risk, McIlroy curled a dramatic approach around the pines and into a greenside bunker, then blasted onto the green to 12 feet and two-putted for bogey to secure the triumph.
"It's nice to have that two-shot cushion instead of the one like I had last year," said McIlroy, who needed a playoff to win in 2025.
McIlroy, 36, yelled with joy and lifted his arms into the air after the triumph and hugged daughter Poppy and wife Erica after walking off the 18th green where she embraced his parents.
Scheffler, a four-time major winner seeking his third Masters victory in five seasons, was on 277 after shooting a 68 to complete a bogey-free weekend.
"Over the weekend I put up a good fight, did a lot of good stuff in order to give myself a chance and ultimately came up a couple shots short," Scheffler said.
England's Tyrrell Hatton and 45-year-old Justin Rose and Americans Russell Henley and Cameron Young shared third on 278.
Rose, the 2013 US Open champion, settled for another near miss after three runner-up Masters finishes.
"I felt like there was an opportunity to do better, so obviously that's frustrating for sure," Rose said.
Rose birdied four of the last five holes on the front nine and led on 12-under but bogeys at 11 and 12 moved McIlroy into the lead to stay.
McIlroy sank a seven-foot birdie putt at the par-three 12th after an impressive tee shot, then added an 11-foot birdie putt at the par-five 13th to seize a three-stroke lead.
"I think the tee shot on 12 and then the tee shot on 13, just to give me the option to go for the green in two," were the day's key shots.
"I made a really good committed swing off the 13th tee, and that enabled me to go for the green in two and to make a birdie there, following the birdie on 12. That was massive," he said.
Four pars and the closing bogey followed to produce the victory.