The agonising miss by striker Adisak, the tournament's top scorer, six minutes into added time denied the Thais a fourth final in a row as he skied the spot-kick over the bar.
Malaysia will meet Vietnam or the Philippines in the two-legged final on Dec. 11 and 15, with the Vietnamese holding a 2-1 lead from the first leg when they meet again on Thursday.
Thailand were looking to extend their championship-winning streak to three this year and Milovan Rajevac's side went in front after 21 minutes when Thitipan Puangchan's goalward header was bundled over his own goal line by Irfan Zakaria.
The move started when Malaysia keeper Farizal Marlias rolled the ball out and ended seven quick-fire passes later with Syahmi Safari smashing a right-foot shot from the edge of the penalty area into the top corner of Chatchai Budrom's goal.
Thailand reclaimed the advantage three minutes after the hour when Pansa Hemviboon scored at the second attempt with a header after the Malaysia defence failed to clear substitute Sumanya Purisai's free kick.
But eight minutes later Norshahrul gave Malaysia the edge in the tie once again when he controlled Syamer Kutty Abba's low cross before smashing his shot beyond Chatchai.
The Thais pushed for a winner, with Pansa's header clipping the crossbar late on before Syahmi's handball earned the home side a penalty - and the defender a second booking - only for Adisak to fire high over the bar as their title hopes ended. (Reporting by Michael Church, Editing by Ken Ferris)
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