The goals for Dortmund were scored by Ilkay Gundogan (22), Pierre-Emerick Aubameyang (29) Kevin Kampl (33rd), Shinji Kagawa (74), Jeremy Dudziak (82) and Marco Reus (90th). The goal for the home side was scored by Gary Steven Robbat in the 40th minute.
The visitors took the lead in the 22nd minute when Gundogan scored with a free-kick beating JDT goalkeeper Mohd Farizal Marlias comfortably.
Five minutes later Dortmund when two goals up when Aubameyang scored with a shot from a low cross by Marcel Schmelzer.
A defensive error by the hosts allowed Kampl to make the score 3-0 in the 33rd minute.
The home side pulled a goal back when Robbat hammered a shot past keeper Roman Weidenfeller in the 39th minute to make the score 3-1.
Japanese international Shinji Kagawa scored from a cross by compatriot Maruoka Mitsuro to make the score 4-1 in the 73rd minute.
Dudziak then scored again for the visitors by beating Mohd Izham Tarmizi Roslan with a shot in the 81st minute and then Reus scored the sixth goal in the 90th minute to complete the rout.
On Tuesday in their first game in Tokyo, Dortmund beat Japanese J-League club Kawasaki Frontale 6-0.