Poonam Rani (39th) and Lily Chanu (46th) scored two second half goals at the Stadium Hoki Nasional to seal India's place in the last-four stage of the eight-nation tournament.
With six points in their kitty, the Indian eves finished their Pool A engagements on second position behind China (nine points).
India will now face Pool B toppers Korea in the first semi-final on Thursday, while China will take on Japan in the second last-four match.
India has earlier spanked Hong Kong China 13-0 in their tournament opener before going down to defending champions China by a solitary goal in their next game.
The Indians looked far from promising in the first half as the Rani Rampal-led forwardline failed to breach the Malaysian defence.
Both the teams created a few chances but they failed to break the deadlock in the first half.
After the change of ends, the Indians came out with more purpose and took the lead in the 39th minute through a field goal from Poonam Rani.
Lily Chanu made the scoreline 2-0 in favour of India in the 46th minute through another field strike.
Thereafter, the Indians played sensibly and denied Malaysia any opening to make a comeback into the match.
