The young Aussies found themselves 3-0 down with 20 minutes remaining before pulling two goals back to set up a thrilling finish.
But despite a host of chances in the dying stages the Joeys were unable to fashion an equaliser and will now face Laos in the 3rd/4th placed playoff.
Ufuk Talay’s side headed into the contest in scintillating form after winning all four of their previous matches, scoring 24 goals in the process.
But a defensively resolute Thailand proved difficult to break down for the Aussies as the scores remained locked at 0-0 at the interval.
And it was Thailand who opened the scoring with two quick-fire goals at the start of the second half to take control of the contest.
Australia pushed forward as they looked to fight their way back into the contest but were caught out on the counter attack with Thailand netting a third to effectively seal the win.
The Joeys were handed a lifeline with 15 minutes remaining when a Thai defender was shown a second yellow card for a late challenge inside the area.
John Roberts made no mistake from the spot to give Australia a glimmer of hope.
And a brilliant solo goal from Dylan Pierias with 10 minutes left gave the Joeys a real chance but Thailand managed to hold on and advance to the final against Myanmar.