On Friday, he was taken all the way to the last by fellow American Jason Kokrak but drove the green at the par four and made a birdie to earn a 1 Up win and a last-16 clash against Mexico's Abraham Ancer.
Morikawa was 4 Up at the turn after birdies on the first, fourth and seventh and a hole-out eagle on the fifth but Kokrak quickly set about clawing things back.
He made an eagle of his own on the par-five 12th and birdies on the tenth, 13th and 15th had him level before Morikawa edged ahead with a gain on the 16th.
A three-putt from the World Number Two on the 17th meant it was all to play for but his tee-shot to 32 feet on the 18th set up a two-putt birdie and victory.
MacIntyre beat Garcia 4 & 2 in the other Group Two match.
Ancer continued his record of having not trailed in a match all week as he beat Webb Simpson 2 Up.
The top seed in Group 15 birdied the sixth and seventh but bogeyed the next as he turned in 1 Up.
Another gain on 11th moved him 2 Up again but Simpson fought back to win the 14th and 16th, only to surrender the 17th with a bogey before Ancer parred the last.
"You're always going out there trying to win, feeling like if you don't win you're not going to advance," said Ancer. "So now it's real. Now you're for sure not advancing if you don't win.
"So I'm excited. I love match play. It's a lot of fun and I'm just looking forward to it."
Bubba Watson and Brian Harman finished All Square in the other Group 15 match.
The Japanese had lost his opening match but he hit back on day two and was a convincing winner over Herbert on Friday.
He won the second and third with pars and then the fourth with a birdie before Herbert hit back with a gain on the next.
Kanaya birdied the sixth and while Herbert picked up a shot on the ninth, Kanaya then won the tenth with a par and made birdies on the 12th and 13th to set up the play-off.
It was advantage to the Australian on the first extra hole as Kanaya had to play out of a bunker sideways but he saved his par and with Herbert three-putting after missing from inside three feet, it was the 56th seed who went through.
"I'm feeling so great," said Kanaya. "I am happy I got through. I'm proud of myself."
Kanaya will face Corey Conners in the last-16 after the Canadian beat Alex Noren 3 & 2 in a winner-takes-all clash in Group Ten.
Tony Finau beat Xander Schauffele 4 & 2 in the remaining Group Seven match.