Chhetri struck in the 39th and 53rd minute, while the promising Jeje Lalpekhlua also found the back of the net in 47th minute.
In response, Safee Sali bagged a brace for the visitors, scroing in the 45th and 59th minutes, but it proved not to be enough for the reigning ASEAN champions at Kolkata's Salt Lake Stadium.
The Indians played positive football and dominated proceedings throughout, indeed their margin of victory could have been greater if not for some inept finishing in the final third.
Midfielders Baldeep Singh, Francis Fernandes, Rocus Lamare and Lalrindika Ralte combined well for India and never allowed Malaysia to settle. India captain Syed Rahim Nabi also starred in what head coach Savio Medeira regarded as a confidence boosting victory.
“The boys played their hearts out. It’s good to end with a victory. We did make quite a few changes in the playing XI and it paid off,” said India coach Savio Medeira.
“The SAFF Championship is knocking at the door and we needed to give a chance to everyone to gauge their match temperament. We didn’t get much time to prepare for the match but the boys rose to the occasion,” he added.
Two-goal hero Chhetri said: “We (India) played well. It’s a special feeling when you score for your country.”
The first friendly between the two teams at Guwahati had ended in a 1-1 draw.