Thailand had beaten the same opponents to win 50-over gold and they gave a much better performance with the bat as they reached 120 for 3 in 20 overs.
Natthakan Chantham was the star as she hit an unbeaten 73 from 61 balls and shared a second-wicket partnership of 104 with Naruemol Chaiwai after a wicket had fallen without a run on the board.
Indonesia also improved with the bat but were restricted to 80 for 6 as five bowlers all took a wicket.
Thipatcha Putthawong finished with 11 wickets in four T20 matches and Natthakan Chatham was leading run-scorer with 115 as well as player of the match.