In the women's competition, top seed Caroline Wozniacki of Denmark battled to a 6-2 3-6 6-1 win over Kaia Kanepi of Estonia to claim her third WTA title of the year.
Berdych, who shocked American second seed Andy Roddick and third seed Fernando Gonzalez on his way to the final, surprisingly had a one-sided 6-1, 6-4 victory over the fifth-seeded Del Potro.
"In this condition and at this level of tennis, I think the most important thing is to... just be 100 percent on the court - then the results can come," said the 23-year-old Czech.Berdych, currently ranked 27th in the world, said his goal was to finish 2008 in or near the top 10.
"I think it happened to me this week and I'm very happy for that. I'm really happy to win here, especially here in Tokyo, I hope I will be here next year."
Del Potro - ranked 12th after a blistering summer during which he won four titles - appeared to be off form, taking an injury time out during the first set and another before the start of the second set.
Del Potro said he had taken some medication, but did not blame the loss on his illness, saying:
"He played much better than me. I was feeling confused (by his play), but he did a great match."
"After the first set I started to play a little better, but it was too late."It was Berdych's first title since winning at Halle in June last year, and his fourth overall, after victories at Palermo in 2004 and Paris in 2005.
On the women's side, the 18-year-old Wozniacki added to her 2008 success, after winning in Stockholm and New Haven in August.
"I feel amazing. I just won another tournament. It's been an incredible year. This is my first title here in Japan and I'm very happy," said a jubilant Wozniacki, ranked 16th against Kanepi's 33rd.Leander Paes and Lukas Dlouhy's bid for a second successive ATP title ended in disappointment after the top seeds were stunned by the Russian-German pair of Mikhail Youzhny and Mischa Zverev in the finals of AIG Japan Open in Tokyo today.
"I think I improved a lot last year."
The unseeded Youzhny and Zverev beat the Indo-Czech pair 6-3, 6-4 to capture their second ATP title together.
It is the second time this year that Youzhny and Zverev have combined to deny Paes and Dlouhy a title win, having also done so when they claimed their maiden ATP title at Halle in June.
(Via news.theage.com.au, Images via Yahoo! Sport, zimbio.com)