Thomas Partey put the visitors in front after just nine minutes in rain-lashed Yokohama before an Emmanuel Boateng penalty early in the second further dented Japan's hopes.
Thomas, who plays in Spain at Atletico Madrid, blasted a free-kick into the bottom corner after a foul by Tomoaki Makino on the edge of the box.
Japan's talisman Keisuke Honda twice went close at the other end, but Boateng stunned the home side by doubling Ghana's lead from the spot six minutes after halftime.
Nishino, the 63-year-old former JFA technical director, threw on playmaker Shinji Kagawa, marking his return to the Japan side after an absence with ankle trouble since the start of the year.
Forwards Shinji Okazaki and Gaku Shibasaki also came off the bench as Japan chased goals but the hosts never really threatened a comeback.
Japan travel to Europe to take on Switzerland on June 6 and Paraguay on June 12 in final tune-ups before facing Colombia, Senegal and Poland at the World Cup.
Nishino names his final 23-man FIFA World Cup squad for Russia on Thursday.
Source: AFP
