Goalscorers Luis Corrales and Emiliano Tade delivered top performances off the bench with Corrales notching his fourth goal of the season to go alongside strikes against Otago United and Waitakere United.
Tade's reputation as an impact player was enhanced when he guided home a header three minutes into the second half.
Corrales rounded off the scoring beating the Matsumoto goalkeeper in a one on one situation midway through the second half.
Yet Matsumoto Yamaga created a number of decent chances in each half with goalkeeper Tamati Williams - and his second half replacement - Jacob Spoonley, both pulling off important stops.
Auckland's winning margin could have been even more emphatic had Pedro Santa Cecilia Garcia managed to score from 8 yards out with the Matsumoto goalkeeper nowhere to be seen.
Matsumoto Yagama FC experienced a meteoric rise through the J.League ranks earning promotion to J.League 2 in 2011 and has inflicted a giant-killing upset 2-0 win over Urawa Reds in the Emperor's Cup two years ago.
The win for the Oceania champions is the fifth time Auckland City have downed professional opposition in a growing list that includes Al-Ahli 2-0(UAE), Central Coast Mariners 3-1(Australia), TP Mazembe (Congo) 3-2 and Japanese clubs Ryuzu Keizai 2-1, and Matsumoto Yamaga 2-0.
Auckland City's Club World Cup opponents Sanfrecce Hiroshima finished their J.League fixture programme off with an away match at struggling Vissel Kobe.
The FIFA Club World Cup playoff between Auckland City and Sanfrecce Hiroshima takes place on December 6 at the Yokohama International Stadium.
The match will be broadcast live on New Zealand's Sky Sports 3 from 11.45pm.