The World Number One started the day with a three-shot lead and ten clear of McIlroy but it was the Northern Irishman who was within three as he carded a stunning 64 to get to seven under.
Many have buckled under the pressure of the back nine at Augusta National Golf Club over the years but Scheffler was able to find another gear, extending his lead so that even a four-putt on the last could not deny him as he signed for a 71 to finish at ten under, three shots clear of McIlroy.
At the start of 2022, Scheffler was 12th in the Official World Golf Ranking and without a win on the DP World or US PGA Tours despite his starring role for the United States in last year's Ryder Cup win.
But he won the PGA Tour's WM Phoenix Open in February and the following month added the title at the Arnold Palmer Invitational.
Just three weeks later he was a DP World Tour and World Golf Championships winner as he lifted the trophy at the WGC - Dell Technologies Match Play, moving to World Number One in the process.
And now, after his fourth win in six starts, he has a Green Jacket, becoming the first player since Christiaan Bezuidenhout in 2020 to win back-to-back events on the DP World Tour, and the first since Jeunghun Wang in 2016 to claim his first two DP World Tour wins in consecutive events.
It is also a third Masters win for caddie Ted Scott, who won at Augusta with Bubba Watson in 2012 and 2014.
“I was so overwhelmed and didn’t know I was ready for this,” Scheffler said. “I cried like a baby this morning.
“I’ve dreamed of having a chance to play in this tournament, I teared up when I got my first invite in the mail. I love this place and if you’re going to choose a tournament to win it would be this."
I can’t put into words what it means that I’ll be able to come back here for a lifetime
He added: "Probably the first time the thought of winning popped into my mind was Friday in the afternoon after we got done.
“I never really make it this far. I always dream of being here and competing. I can’t put into words what it means that I’ll be able to come back here for a lifetime, hopefully, and I can’t speak highly enough of this place."
Scheffler produced a brilliant chip from over the back of the first green to help him save par after his tee-shot had put him in trouble but saw his lead cut to two as Smith put his approach to 12 feet and made the putt.
A two-putt birdie on the par-five second made it a birdie-birdie start and Smith was within one but there was a two-shot swing at the next as, after both men played poor first and second shots, Scheffler holed an incredible bump-and-run and Smith failed to get up and down.
Another Smith bogey on the fourth after finding the sand meant Scheffler led by four, with both players birdieing the seventh from inside four feet.
The roars around the course could not have been missed by the final group and they were coming from the patrons watching McIlroy make a huge move.
He had birdied the first from nine feet and two-putted the third after driving right up to the fringe but really came alive around the turn.
The 32-year-old holed a 30-foot right-to-lefter from the fringe at the seventh, recovered from a poor tee-shot at the eighth to take advantage of the par five and then chipped in at the tenth before putting his second to ten feet at the 13th to set up an eagle that put him one behind Smith.
He was tied for second and just four off the lead as both members of the final group bogeyed the tenth but a poor tee-shot meant he could not take advantage of the par-five 15th.
Smith birdied the 11th from 15 feet but then, like so many contenders down the years, he found the water at the 12th and a triple-bogey ended his chances.
A run of four pars looked to have ended McIlroy's as well but he holed a spectacular bunker shot on the last, using the contours of the green to record a birdie, spark wild celebrations and set the target at seven under.
Scheffler was relentless, however, putting an approach to five feet at the 14th and getting up and down at the next for back-to-back birdies before he gave both those shots back with a double-bogey on the last.
Smith followed his double on the 12th with a bogey on the 14th but then birdied the 15th and 16th as he signed for a 73.
Lowry overcame a triple-bogey on the fourth with birdies on the second, sixth, eighth, ninth, 13th, 15th and last, also dropping a shot on the 12th in a 69.
Morikawa created wonderful scenes on the last, following playing partner McIlroy in holing out from the bunker for a sixth birdie of the day to go with an eagle and three bogeys in a 67.