The Indian colts came from a goal down to win their second consecutive match of the tournament at the Taman Daya Hockey Stadium.
Malaysia scored early through Firdaus Omar (3rd minute) but India's Dilpreet Singh (20th, 43rd) found the bet twice to enable India take full points from the encounter.
It was the Malaysian side who started the match aggressively as they displayed some attacking hockey which led to an early penalty corner in the third minute and drag- flicker Firdaus Omar converted the chance past Indian Goalkeeper Pankaj Rajak.
In the second quarter, India started strongly as they looked to make a comeback into the match.
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Indian managed to draw level in the 20th minute when a long pass to Dilpreet Singh was well controlled by the forward on the right flank, after which he turned inside and hit a fierce shot that was deflected off the Malaysian goalkeeper Muhamad Mat Deris on to the back of the net.
It was the Indian team which had the momentum on their side in the second quarter but they could not take the lead as the teams went into half-time locked at one goal apiece.
Malaysia looked to threaten on the counter but were unable to make attacking forays as they were not efficient in their opportunities.
India were looking strong offensively as they maintained possession to put pressure on the Malaysian defence which finally led to a second goal in the 43rd minute when Maninder Singh showed his stick skills on the right flank and passed the ball inside the circle on to Dilpreet who did the rest.
India ended the third quarter with a 2-1 lead after Dilpreet's strike, his fourth goal of the tournament.
India will next play USA in their third match on Wednesday.