Koo Keat Kien and Choong Tan Fook made it 2-0 with victory over Shintaro Ikeda and Shuichi Sakamoto with Wong Choong Han sealing Japan's fate when he beat Kenichi Tago.
Japan was disappointed after a thrilling come-from-behind win against Denmark in the elimination round, but coach Park Joo Bong was content with what they had achieved.
"In the last few meetings, my players have demonstrated a lot of fighting spirit," he said.
Malaysia is in danger of being left behind by the world's major badminton powers unless the country can find a fresh pool of talent, the country's badminton chief has said.
Badminton Association of Malaysia president Nadzmi Salleh told local media that Olympic status meant more countries were producing top-quality players, as witnessed at the Thomas and Uber Cup finals being played in Indonesia.
"Badminton is gaining popularity worldwide and many countries are now taking notice since it became an Olympic sport," Nadzmi told the New Straits Times on Wednesday.
"From what I have seen in the Thomas Cup, countries like Japan, Denmark and South Korea are improving fast."
The men's Thomas Cup and Uber Cup for women are among the most prestigious tournaments in world badminton.
Malaysia last won the Thomas Cup in 1992 when the team tournament was held in Kuala Lumpur but appears unlikely to add to that triumph in Jakarta this week.
World No 2 Lee Chong Wei is the country's leading male singles player but there are no other Malaysians ranked in the top 10.
Nadzmi said most Malaysian players lacked the ability to think on their feet, unlike their rivals from other countries.