With the victory in the team sprint, the Malaysians regained some confidence after their prospects came under question following their defeat in the Asian Championships in Sharjah in April.
Japan, who fielded veteran Kitatsuru Tsubasa with Tomohiro Fukuya and Kazuki Amagai, fired the first salvo by topping the time sheets in qualifying with a time of one minute 18.018s on the 400m outdoor concrete all-weather track.
Malaysia, the Asian team sprint champions last year, with Edrus as starter, Azizul on the second lap and Rizal as the anchor, clocked 1:18.374s to book a showdown in the final with Asian champions Japan. South Korea were third.
In the final, all three got their acts together and delivered a super fast 1:17.183s to pip the Japanese, who clocked 1:17.247s, to the gold medal.
"This was a good start to our build-up towards the Asian Games and Commonwealth Games. The team sprint which we are banking on heavily showed they are getting their act together after the disappointment at the Asian Championships," said team manager Datuk Naim Mohamad.
"This is the first competitive outing since the team began the final phase of preparations for the big two events in October and November, so the results are promising.
"We decided to send just a small team of three riders, so with a gold, two silvers and a bronze medal, it is a healthy return."
Edrus had earlier got himself a second Asia Cup medal when he won the silver in the 1km time trial behind Amagai, while India's Bikram Singh Okram took the bronze.
On Saturday, Azizul and Edrus won the silver and the bronze in the 200m sprint.
Azizul lost to Tsubasa in the final, while Edrus beat Fukuya in the race for bronze for his first personal Asia Cup medal.