This meeting is deemed to be the warm-up match for Malaysia, who ranked 13 in the world, before facing Russia in the second match on Sunday.
Malaysia does not have problems against Chile but had to wait until the 18th minute to open the scoring after a penalty corner by Mohd Razie Rahim.
However, Chile early spring a surprise when they equalized two minutes later by Jan Richter, with a penalty corner.
Chile's actions did not break the spirit of Tai Beng Hai's men when Faisal Saari scored Malaysia's second goal in th 22nd minute.
Malaysia back in the second half by changing the rhythm to a more aggressive game to tame the Chilean team with three more goals through Hafifihafiz Hanafi in the 49th minute, Mohd Razie in the51st minutes and Mohd Amin Rahim in the 61st minute.
Malaysia needs to win the qualifier to book a ticket to the London Olympics in July.
