The Eurasia Motorsport Oreca Nissan completed the podium in third, one lap back.
Clearwater Racing also continued its undefeated streak in GT, with the Rob Bell, Weng Sun Mok and Keita Sawa-driven McLaren 650S GT3 cruising to a one-lap victory over the No. 91 Team AAI BMW Z4 GT3, which featured Dirk Mueller on the driving strength.
The No. 90 Team AAI Mercedes SLS AMG GT3 completed the podium in third.
All four of the junior prototypes faced issues in Malaysia, with the two Wolf GB08 CN cars finishing 12th and 13th overall, with the LMP3 machines classified in 15th and 16th.
The Fuji class-winning DC Racing Ligier JS P3 was classified ahead of the Team AAI ADESS 03 at the end, although nearly 20 laps behind after spending nearly 30 minutes in the garage with a halfshaft failure.