The Urawa Red Diamonds of Saitama, Japan defeated Sepahan F.C. of Esfahan, Iran 2-0 in Saitama (3-1 on aggregate).
Story from the official site here.
Although the story says that the Reds are the first Japanese side to win the Champions League, the league itself has only been around since 2002. Before that, there was the Asian Club Cup where the last Japanese champion was Jubilo Iwata back in 1999.
Yuichiro Nagai and Yuki Abe scored the goals for the Reds.