The Roar cannot make it out of their group despite a gallant effort in Thailand from a second-string side fielded by coach John Aloisi, who has saved most of his best players for Sunday's grand final qualifier against Melbourne Victory.
But the biggest concern surrounds Young, who was forced off after suffering a large, deep cut to his arm on Wednesday night in a nasty collision with the goalpost as Muangthong scored their 37th-minute opener.
Former Newcastle United striker Xisco deftly headed home Tristan Do's cross via the upright, into which Young clattered as he tracked the flight of the ball through the air.
The 31-year-old, who came into the team after first-choice goalkeeper Michael Theo injured his knee last week, appeared to catch his elbow on a dangerously-exposed and rusty hook on the post, which was left smeared in blood.
The same goalmouth was also inspected at length by officials before the match who found the net was not properly secured, leading kick-off to be delayed by five minutes.
Youngster Tomislav Bilic was brought on for Young, who could be in doubt for Sunday's clash with Victory at AAMI Park if the wound is as serious as it appeared to be and doesn't heal in time.
The Asian Football Confederation will be expected to come down hard on Muangthong if old or faulty equipment is found to be the cause of injury.
Brisbane Roar managing director Mark Kingsman tweeted: "How can this be allowed in our elite club competition?"
Aloisi rotated his squad heavily with Young, Thomas Broich, Nick D'Agostino and Luke DeVere the only starters for Brisbane who were involved in Friday's elimination final win against Western Sydney Wanderers.
Only D'Agostino played the full 90 minutes, which the Roar grew into after a meek start.
But they ultimately lacked the poise and polish of the Thai Premier League champions, who had most of the play and the better of the chances, and the visitors faded badly late on.
Chanathip Songkrasin iced the victory with his 83rd-minute goal, guaranteeing them a spot in the ACL's knockout stage for the first time, while Teerasil Dangda delivered the final blow six minutes later.