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
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.