Atletico Madrid midfielder Thomas Teye Partey and debutant Emmanuel Boateng scored to hand the Black Stars the 2018 Kirin Challenge Cup at Kanagawa's Nissan Stadium, Yokohama.
While hosts coach Akira Nishino used the encounter to assess players ahead of naming of his final World Cup squad on Thursday, Kwesi Appiah's outfit are on a preparatory curve ahead of September's clash with Kenya in the 2019 Africa Cup of Nations qualifying.
Ghana's captain of the day Partey broke the deadlock in the eight minutes, curling a free-kick from outside the box around the wall into the net.
Japan were seemingly awoken by the goal, but found the Black Stars' central defensive pair of Nicholas Opoku and Rashid Sumaila as well as goalkeeper Richard Ofori hard to beat.
After the hosts made two quick attempts to snatch the equalizer just after recess, Ghana increased their tally in the 51st minute through youngster Boateng .
On his international debut, the Levante striker buried the ball into the net from six yards, having won a penalty after being hacked down by goalkeeper Eiji Kawashima
The 22-year-old was substituted in the 82nd minute, giving way for Bayern Munich striker Kwasi Okyere Wriedt to make his own debut for the country of his parents.
The result has put Ghana on two wins as against Japan's four in six international meetings between the two sides at senior level.
Ghana next take on another World Cup-bound side Iceland on June 7.