Olivier Giroud continued his fine pre-season form with an early goal, before Ryo Miyaichi delighted the home fans with a penalty and Theo Walcott netted a third.
However, Nagoya did pose a challenge to the Premier League outfit and Kisho Yano earned his team a goal with a towering header after 72 minutes.
Arsene Wenger fielded a strong Arsenal side for the match, including first-team stars such as Giroud, Walcott and Mikel Arteta, while Bacary Sagna partnered Per Mertesacker in the heart of defence.
And they made a superb start as an unmarked Giroud planted a firm header home from Tomas Rosicky's cross.
The goal marked the sixth in pre-season for the Frenchman, as he looks to convince Wenger of his talents amid rumours that the London club are targeting strikers.
Arsenal's advantage was then doubled before half-time came as Giroud won a penalty which 20-year-old Miyaichi kept his composure to fire into the top corner, to the loud acclaim of the Japanese support.
The break brought a number of changes and it paid off for the visitors as Walcott scored a close-range effort after a brilliant reverse pass from exciting 16-year-old Gedion Zelalem.
The last goal of the game saw the home side grab a consolation with 18 minutes to go through 29-year-old Yano, who nodded in from a corner.
Arsenal will face Urawa Red Diamonds on Friday before returning home to host the Emirates Cup which also includes Napoli and Galatasaray.