All three goals were scored in second half with Harmanpreet (41st, 56th) putting India ahead before Shahril Saabah (68) pulled one back for the hosts.
It was second win in a row for India, following their triumph over Argentina.
The Indian colts dominated the match from the first minute and penalty corner specialist Harmanpreet's two conversions helped the team earn three more points.
With 9 points, defending champion India lead the table, ahead of Great Britain (8) and Argentina (7).
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Arman, Sumit and Gurjant kept the defenders busy with their short passes and tried hard to penetrate the ball in the goal-box.
After a series of attacks, India earned two penalty corners in a short span but both were saved by Malaysian goal-keeper Ridzwan Azmi. Ridzwan hold the goal-posts with the help of his team-mates and successfully restricted India's fierce attacks. The first-half finished goalless at 0-0 score-line.
Skipper Harjeet Singh led the midfielders pack, consisting of Santa Singh, Nilakanta Sharma, Simranjeet Singh and Manpreet, and attacked the opponents from both right and left flanks.
In the 41st minute, India earned a crucial penalty corner and drag-flicker Harmanpreet converted it successfully into the first goal of the match.
Conceding a goal, the Malaysians counter-attacked in the next moment and earned a penalty corner, which was perfectly thwarted by Indian custodian Suraj Karkera. Indians charged back with their speedy attacks and earned two more penalty corners.
After the goal, both the teams fought harder as Indians were trying to score more where as Malaysians played harder to open their account.
The neck-to-neck battle went on till the last moments of the game and in the 68th minute, Malaysia managed to earn a penalty corner, which was converted into their lone goal by Shahril Saabah. Indians held the game till the final whistle and won their fourth league match by 2-1.