Perez, a winger for Barca's B team, slotted through goalkeeper Daiya Maekawa's legs on the hour mark after a neat one-two with Malcom to open the scoring. Malcom came close to adding a second, thumping the bar from close range, before Perez netted his second late on as Barca picked up their first win of preseason following Tuesday's defeat to Chelsea.
Ernesto Valverde's side now return to Spain, where they will link up with the South American players that were absent from the tour of Japan due to the Copa America, including Lionel Messi and Luis Suarez.
They face Arsenal next weekend at Camp Nou in the Joan Gamper Trophy, before heading to the United States for two matches against Napoli.
Valverde named new signing Antoine Griezmann as Barca's central striker for the second time in a week at The Noevir Stadium in Kobe, while former Blaugrana players Iniesta, David Villa and Sergi Samper all started for Vissel.
Iniesta, 35, impressed in the first half. He came close to breaking the deadlock early on with a curled effort from the edge of the box which bent just wide.
The Spanish champions made 11 changes at the break, with Frenkie de Jong and Ousmane Dembele introduced, but it was an academy graduate who made the difference.
Perez found the breakthrough after a neat exchange with Malcom and then closed the scoring with a drilled finish across Maekaw from just inside the area in the 86th minute.
In between the two goals, Carles Alena twice came close, failing once with an audacious chip, and Malcom smashed the woodwork in an impressive cameo.