The pair of Loh Kean Hean and Terry Hee (world ranked 61) put up a strong fight against the world number 14 duo of Muhammad Shohibul Fikri and Bagas Maulana, but were edged 21-15, 21-17.
Jason Teh grabbed a point for Singapore after beating Christian Adinata 21-15, 12-21, 21-14.
Despite a spirited fight by youngsters Nge Joo Jie and Johann Prajogo, Indonesians Pramudya Kusumawardana and Yeremia Rambitan closed out the tie 21-18, 21-16.
In the women’s team semi-finals, world number 34 Yeo Jia Min notched up an impressive win over Thailand’s world number 23 Lalinrat Chaiwan 21-15, 21-6 to get Singapore off to a strong start.
But the defending gold medallists won the next three matches for a 3-1 victory.
Jongkolphan Kititharakul and Rawinda Prajongjai beat Jin Yu Jia and Crystal Wong 12-21, 21-9, 21-14, while Supanida Katethong dispatched Insyirah Khan 21-11, 21-8.
Benyapa and Nuntakarn Aimsaard wrapped up the overall win for Thailand when they swept aside Heng Xiao En and Elsa Lai 21-6, 21-7.