Giovani broke the deadlock in the 75th minute, taking a superb through ball from Ronaldinho and sliding a shot past goalkeeper Tetsuya Enomoto.
Barcelona had started with recent signing Thierry Henry alongside Ronaldinho and Samuel Eto'o in a fearsome front line but the Spanish side lacked a cutting edge on a humid evening in Yokohama.
Eto'o had a seemingly legitimate goal ruled out for offside while Henry, still coaxing himself back from an injury-plagued final season at Arsenal, was substituted at halftime.
Ronaldinho went close and Eto'o smashed a shot against the post within 10 minutes of the restart as Barcelona tried to inject some urgency into their play.
With 15 minutes to go they finally got their reward through Giovani, the 18-year-old who had also opened the scoring in Barca's 3-0 win over Beijing Guoan on Sunday.
Former World Player of the Year Ronaldinho received a standing ovation from a crowd of 56,000 when the Brazilian was taken off three minutes before the end.
The Catalans, denied a third straight Spanish title by Real Madrid on the final day of last season, finish a tour that has been criticised by some of the players against a Mission Hills XI in Hong Kong on Friday.