Wirtz, signed in a high-profile move earlier this summer, brought Liverpool level in the second half after Asahi Uenaka had put the relegation-threatened Japanese side ahead.
Uenaka's well-taken finish, assisted by Ren Kato, briefly stunned the Premier League giants, who were looking to bounce back after a 4-2 defeat to AC Milan in their previous outing.
The German midfielder's equaliser was the product of quick transitional play, initiated by Curtis Jones winning possession high up the pitch.
Mohamed Salah played a key role in the move, indirectly assisting with a clever layoff as Wirtz coolly finished to mark his first goal in Liverpool colours.
Wirtz's strike sparked a turnaround, with teenager Trey Nyoni netting the winner - also his first senior Liverpool goal - after a sharp assist from Jeremie Frimpong.
Rio Ngumoah, just 16 years old, sealed the result in the dying minutes with a stunning solo effort from the edge of the box, capping an impactful 27-minute cameo.
New signing Hugo Ekitike made his debut, linking well with Salah and Cody Gakpo but spurning multiple chances, including an inventive backheel saved by Yokohama goalkeeper Park Il-gyu.
Gakpo hit the post early and later missed a one-on-one, while Darwin Nunez, who replaced Ekitike at the break, also squandered a close-range opportunity.
Newcastle United have firmly rejected speculation surrounding Alexander Isak's potential transfer to Liverpool, with the club's owners, the Public Investment Fund (PIF), insisting the striker will remain at St James' Park.
Bayern Munich have completed the signing of Luis Diaz from Liverpool with the Colombia international penning a four-year contract with the German champions.
Liverpool's pre-season preparations have taken a few unexpected turns as the squad gets ready to face Yokohama F Marinos in the final match of their Asia tour on Wednesday.
Tottenham Hotspur's hopes of landing Real Madrid's star winger Rodrygo have been dashed, as the Brazilian forward has his sights set on a more prominent destination, according to recent reports.
