
Japan, ranked world No 4, took an unassailable 3-1 lead after winning the first two singles and the second doubles matches at the tournament in Horsens, Denmark.
Malaysia, as runners-up, now face the formidable task of meeting one of the group winners when a fresh draw is made after the group stage concludes.
Leong Jun Hao put in another disappointing display, losing to Kodai Naraoka 21-11, 21-15 in the opening match.
Aaron Chia-Tee Kai Wun then beat Kakeru Kumagai-Hiroki Nishi 16-21, 21-14, 21-19, before Justin Hoh fell to Yushi Tanaka 21-15, 21-12.
Soh Wooi Yik-Nur Izzuddin Rumsani then lost to Takumi Nomura-Yuichi Shimogami 21-14, 19-21, 19-21.
The final game will see Lee Zii Jia take on Koki Watanabe.