The home side looked set to take a lead into next week's second leg when super sub Adrian Segecic cancelled out Richairo Zivkovic's penalty then scored a second 19 minutes later in the second half at Allianz Stadium on Wednesday.
Segecic has made a habit of turning games late on for Ufuk Talay's side, scoring seven goals from the bench in his past five substitute appearances.
But just as Sydney were dreaming of heading to Thailand next week to defend a lead in a bid to secure a spot in the quarter-finals, disaster struck.
Thitipan Puangchan fired a close-range shot from a tight angle past Harrison Devenish-Meares to send a small section of travelling Bangkok supporters that formed the 5,131 crowd into a frenzy.
Sydney were crestfallen and frustrated and understandably so after having two penalty appeals turned down by referee Yamashita Yoshimi in the first half.
The first came when left-back Jordan Courtney-Perkins was bowled over in the Bangkok box, then Thossawat Limwanasathian brought down Sydney frontman Patryk Klimala.
Both times Yoshimi waved play on despite VAR being available for the Japanese official to check.
Yoshimi would eventually signal a penalty but it came early in the second half when Bangkok's Muhsen Al-Ghassani raced onto a long ball over the top of the Sydney defence.
The Omani international was felled by Devenish-Meares inside the box as he attempted to go around the Sydney goalkeeper.
Bangkok striker Zivkovic converted from the spot to give the away side a 50th minute lead.
Talay immediately went to his bench with Douglas Costa and Segecic thrown on to give the home side more spark in the final third.
It worked instantly with Costa playing in Segecic and the young playmaker guiding the ball past Khammai for a 60th minute equaliser.
Suddenly Sydney had a spring in their step and nobody was oozing more confidence than Segecic, who was allowed far too much space by the Thai side.
The midfielder let rip from the edge of the Bangkok box in the 79th minute to put his side in the lead.
But just as Sydney were preparing to celebrate a come-from-behind win, Puangchan struck to salvage a draw.
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