Iniesta and Villa were almost unplayable at the Noevir Stadium in Kobe, winding back the clock with indelible link-up play in the final third.
The star duo's withdrawal at half-time, however, soon swung the pendulum back in Barcelona's favour, with the likes of Perez, Ousmane Dembele, Malcom and new signing Frenkie de Jong all joining the fray for the second half.
Despite some spirited defending from the home side, a neat one-two between Perez and Malcom on the hour mark manufactured their undoing.
With Perez through and one-on-one with the onrushing Daiya Maekawa, the 21-year-old held his nerve to put manager Ernesto Valverde at ease.
Barcelona assumed full control of the match following Perez's neat finish and the substitute duly doubled his tally with a driven shot five minutes from full-time.
Saturday's contest will likely be the first of many pre-season fixtures between the two sides, who announced a formal partnership before the match.
Barcelona will next face Arsenal on August 5.
