For a third successive year, Scheffler began the week on 10 under par as the leader of the FedEx Cup standings, two clear of Xander Schauffele in second, with Morikawa among a group on four under in the staggered start.
And he stayed ahead through the first three rounds to set up what looked like a straightforward final round.
His five-shot lead was six after Morikawa bogeyed the first hole.
However, Scheffler made uncharacteristic errors as he recorded successive bogeys on the seventh and eighth holes that allowed Morikawa, who birdied the fourth, sixth and eighth holes, to close to within two.
A wayward drive left Scheffler hacking out from underneath a conifer tree down the left of the seventh, while he mis-hit a greenside bunker shot on the eighth that squirted out right and ended up further away from the hole.
“I was a bit frustrated because it was quite a basic shot, but I’ve shanked it from a similar lie before,” he said.
“Ted [Scott, Scheffler’s caddie] did a good job of helping me reset. He gave me a nice pep talk there on the back of the eighth green because I looked at him like, ‘man, I don’t know about this, this isn’t looking so hot right now’.
“He gave me a little pep talk and then I was able to hit a really nice iron shot in there [on nine] and got things rolling.
“He really is a huge part of the team. I don’t know if I’d be able to do any of this without him on my bag.
“And then I did some really nice stuff to finish this tournament off.”
That “nice stuff” started on the ninth hole with a birdie, and two more followed on the 10th and 11th as Scheffler surged four clear.
Morikawa responded with a birdie on the 13th, but Scheffler drained a 15-foot eagle putt on the next to re-establish his five-shot lead, and he parred his way home to secure his first FedEx Cup title.
“Nothing fazes him,” said Morikawa, who collected $12.5m for finishing runner-up.
“Whether I was gaining some ground or he was gaining ground, it didn’t change how he walked or how he played or how he went through every shot.
“That’s something to learn. His mental game is a lot stronger than a lot of people know.”
Sunday’s prize money takes Scheffler’s official earnings for the season to around $54m and he has broken the PGA Tour record in that respect for a third season in a row.
It has also been quite the year off the course for Scheffler, who became a father for the first time in May and then just days later was arrested on the morning of the second round of the US PGA Championship for an alleged traffic offence as he arrived at the course.
He was taken to the police station and charged with assaulting a police officer but made it back to the course in time to play. All charges were later dropped.
“I feel like I’ve lived almost a full lifetime in this one year,” said Scheffler “It’s been nuts.”
Meanwhile, Northern Ireland’s Rory McIlroy finished the best of the UK golfers. He started the week level with Morikawa on four under and closed with a five-under 66 to end joint ninth on 16 under.
Scotland’s Robert MacIntyre had six birdies on his back nine as he shot a 64 to end 11 under, one ahead of Tommy Fleetwood who sneaked into the top 20 with a 67.
Fleetwood’s fellow Englishman Aaron Rai, who won his first PGA Tour title in August, hit a closing 70 for a total of six under.
