Australian Herbert got the job done at the second extra hole, recovering from an errant tee-shot before holing from 12 feet to banish the memory of the travel issues which saw him arrive late into Japan.
Extra holes were required after both players finished the tournament on 15 under par following a thrilling final round in the historic first event to be co-sanctioned by the DP World Tour and Japan Golf Tour Organisation.
The win takes Herbert to fourth on the Race to Dubai Rankings in Partnership with Rolex and earns him a first title since the 2021 Dubai Duty-Free Irish Open.
He said: "It's great. Obviously coming on board as an ambassador for ISPS Handa this year, it's great to win an event with them as the title sponsor.
"It's a real honour. And just to be back in Japan and win as well. I've come here so many times and loved it so to get back here and win, it means a lot.
"I think it's cool to be able to win everywhere and have a lot of good memories from all the spots in the world where you have played."
Speaking about the up-and-down that earned him victory at the second play-off hole, Herbert said: "Pretty special. I got pretty lucky over there on the right to get a good lie after we dropped it.
"Nick (caddie Nick Pugh) gave me the number and it was basically perfect. It was exactly what you'd want off that lie.
"So it was good to hit a good shot in there. And then my hand was shaking all over the place just to get the putt started on line, and to have it fall in was pretty cool." DP World Tour