Matthias Jaissle's side became only the second team to retain the trophy in the Asian Champions League era.
The club is led by a former high-school coach and plays at a homely tree-lined stadium in front of an average of 14,000 fans.
The Emirati side lost 1-0 in Jeddah on Tuesday
Ahead of Machida's win, Vissel Kobe coach Michael Skibbe had questioned whether clubs from Japan could compete with their counterparts from cash-rich Gulf state leagues.
In other action, Machida Zelvia earned a 3-1 win over Gangwon FC while Sanfrecce Hiroshima drew with Chengdu Rongcheng.
It is the latest success for manager Go Kuroda, the former high school coach who has brought his golden touch to the professional game.