Harmanpreet Singh converted a couple of penalty corner while the experienced Faizal Saari reduced the deficit for Malaysia immediately after the start of the second quarter.
Another Singaporean shooter Tessa Neo was eliminated in the first round of the finals, after scoring 57.3 in the women's 10m air rifle event at Commonwealth Games.
The 257-kilometre race, called the "Hell of the North," includes 29 sections of cobblestones, which require special control of the bicycle and more effort than a usual road race.
Starting the race from the ninth position due to a five-place grid penalty over a gearbox change, the defending champion - Britain's Lewis Hamilton - rounded out the podium.