The Canberran will captain the side in just his third Test, linking with Force teammate Carlo Tizzano and No.8 Rob Valetini in the back row for Saturday's match at the National Stadium.
With regular skipper Harry Wilson to start on the bench in one of 13 personnel changes to the Wallabies outfit that completed the Rugby Championship, Champion de Crespigny will be the fifth captain under Schmidt's two-year tenure.
"Nick has captained Sydney University in the past. He was vice-captain of the Western Force when they played against the British and Irish Lions, so he's had recent leadership experience," Schmidt said on Thursday.
"He's part of our leadership team and he'll be really well supported by Jeremy Williams and Lukhan Salakaia-Loto, who will be looking after the lineout.
"And obviously with (halves) Jake Gordon and Tane Edmed playing for the Waratahs and playing a couple of Tests together, they will also be really supportive for Nick.
"I've got some experience."
Schmidt defended his decision not to hand the captaincy to Gordon or Williams, both skippers for their Super Rugby sides, after Gordon had been earmarked to lead the Wallabies in the Lions series before being injured.
"One of the things was Jake has only had one game back really, and is very focused on trying to get his own game right," the coach said.
"Nick has been with us consistently week to week throughout and is part of the leadership group anyway, so it was a natural enough progression for him.
"Particularly in the context that Jeremy Williams and Lukhan Salakaia-Loto will be leading the lineout, and Jake and Tane will be running the team.
"Nick is very much a leader of his actions and he'll want to be in the thick of the action as much as he can be."
Queensland prop Zane Nonggorr has earned his first Test start in his 17th appearance for his country, combining with Angus Bell and Josh Nasser in the run-on front row for what is the first of five consecutive matches on the end-of-year tour.
Salakaia-Loto and Williams are the starting locks for what will be the Wallabies' first ever Test against Japan in Tokyo.
Wiradjuri man Dylan Pietsch returns from a jaw fracture to start on the left wing, with fellow Olympian Corey Toole selected on the right edge.
Andrew Kellaway also returns from injury to be selected at fullback and finalise the back three.
Reds pair Hunter Paisami and Josh Flook will form a familiar midfield combination.
Aidan Ross has the potential to become just the fifth man to represent both Australia and New Zealand in Test rugby, named as a likely debutant as the replacement loosehead prop.
With young guns Joseph-Aukuso Suaalii and Max Jorgensen being rested after a huge 2025 Test campaign, Schmidt admitted there was a danger in making so many changes.
"There is a risk," he said.
"Part of the job of the coaching staff is to manage risk as best we can, and if we don't give opportunity to the squad, then I think we start to lose that energy toward the end of a five-Test window, particularly when you're travelling such long distances and jumping time zones.
"Fatigue becomes pretty apparent within two or three weeks, let alone five consecutive weeks, let alone on the back of the Test matches that we've had already.
"So combining those things together, we massively respect for Japan. They've come very close to beating big teams - bigger teams than us - in the past.
"So we are very conscious of that, and that's going to be the challenge for the players who are selected."
Wallabies: Angus Bell, Josh Nasser, Zane Nonggorr, Jeremy Williams, Lukhan Salakaia-Loto, Nick Champion de Crespigny (capt), Carlo Tizzano, Rob Valetini, Jake Gordon, Tane Edmed, Dylan Pietsch, Hunter Paisami, Josh Flook, Corey Toole, Andrew Kellaway. Res: Billy Pollard, Aidan Ross, Tom Robertson, Josh Canham, Harry Wilson, Ryan Lonergan, Hamish Stewart, Filipo Daugunu
