The twice-major champion, who began the day two shots off the lead at Narashino Country Club, rattled off seven birdies to card a bogey-free 63 and finish on 14-under overall.
It gave him his sixth win on the US PGA Tour and his first title since the 2021 DP World Tour Championship in Dubai.
"People start asking questions and they start asking why," said Morikawa, whose last US PGA Tour win was the 2021 British Open.
"I had to really look back and ask myself what's wrong - what's the why, what's the reasoning behind finishing second or fifth versus a win.
"This win means the world," he added.
Eric Cole and Beau Hossler finished in a tie for second on 8-under.
Morikawa was playing his first tournament since being part of the American team that failed to retain the Ryder Cup in Rome.
He led after the first round of the 78-man, no-cut event on the outskirts of Tokyo but faded before roaring back into contention with five birdies on the last six holes in the third round.
He picked up where he left off on the final day, hitting four birdies on the front nine to surge past overnight leader Justin Suh.
He closed out the win with one last birdie to set a new record for the tournament's largest margin of victory.
"Everything just kind of clicked," said Morikawa.
"We were able to not make any errors really, make the par putts when needed, and it was nice to finish off that front nine with a birdie on eight and nine."
Suh faded badly, carding a final-round 74 to finish on 5-under.
Xander Schauffele, who was also playing his first competition since the Ryder Cup, finished on 2-over.
The Tokyo Olympics champion was only three strokes off the lead after two rounds but plummeted down the leaderboard the following day and carded a final-round 71.
Defending champion Keegan Bradley finished on 1-under, while 2021 winner Hideki Matsuyama was 5-over.
The $8.5 million (£7 million) Zozo Championship was established in 2019 as the first US PGA Tour tournament in Japan.
Thousands of Japanese fans turned up to watch Tiger Woods win the inaugural title for his 82nd US PGA Tour victory - equalling Sam Snead's 54-year-old record.
