Prolific Malaysian Safee Sali broke the deadlock in the 54th minute, and although Indonesia scored twice through Mohammad Nasuha (71) and Muhammad Ridwan (88) it was not enough to overturn the 3-0 lead established from Sunday's first leg in Kuala Lumpur.
Malaysia were runners up in the first final in 1996 but have failed to reach the trophy game since then while Indonesia have now finished second on four occasions without winning.
The cup is a biennial competition organised by the ASEAN Football Federation (AFF) and contested by the national teams of southeast Asia.
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