
The victory comes fresh after the 33-year-old’s silver medal triumph at the Olympic Games in Rio de Janeiro last month.
In the final, the world No 1 took one hour and 10 minutes to tame his third seeded opponent 21-18, 15-21, 21-16.
In the first set, Chong Wei, the top seed, was trailing 8-11 before he found his rhythm to take the set in 21-18.
In the second set, Jorgensen, ranked fifth in the world, bounced back to win 21-15 and took the battle to the rubber set.
Chong Wei was leading narrowly in the third set before he started to pull away at 11-8 to finish the match with the 21-16 win.
He was the Japan Open champion in 2014, 2013, 2012, 2010 and 2007.