Mohd Safee Sali was the star for the home side, opening the scoring after a tight first half and adding a third after substitute Mohd Ashari Shamsuddin had doubled Malaysia's lead.
It was a wonderful turnaround from Malaysia, who lost 5-1 to the same opponents in the group stages in Jakarta on December 1.
Safee put Malaysia ahead on the hour mark and Ashari made it 2-0 eight minutes later. Safee put the game, and possibly the tie, out of Indonesia's reach with 17 minutes to go.
The match was stopped for eight minutes in the second half when the visiting players complained to referee Toma Masaaki that the home fans were shining laser lights into their eyes.
The second leg takes place in Jakarta on Wednesday night.