The Thai outfit, who drew 2-2 with the Bulls in Thursday night's second leg will advance to the quarter-finals and face Singaporean side Tampine Rovers after starting at Campbelltown Sports Stadium with a bang.
Omani striker Muhsen Al-Ghassani scored after 90 seconds to leave the hosts with a mountain to climb.
Al-Ghassani doubled Bangkok's lead in the 36th minute before Walter Scott jagged one back for the Bulls just before halftime.
After having a penalty appeal turned down midway through the second half, Harrison Sawyer added another goal for Mile Sterjovski's side in the dying stages but it was a case of too little too late.
"Conceding that early is just a sucker punch," said Macarthur skipper Luke Brattan.
"Even then at 3-0 down, we still had a lot of confidence, a lot of belief.
"It's just something that we switch off in key moments and get punished."
Macarthur had looked a strong contender to go deep into the ACL2 - where the winner nets US$2.5 million ($A3.5 million) in prize money - after topping their group.
But they will now turn their attention to their A-League Men campaign.
The Bulls sit fifth in a logjam of clubs and trail leaders Newcastle by eight points heading into Sunday's away trip to face the Jets.
"The boys gave a lot of effort tonight, we just lacked a bit in the final third," Sterjovski said.
"I felt like there were a lot of calls that went against us and a lot of time wasting, the penalty could have gone either way, I'd have to see it again.
"I believe in the players and their qualities but it's about how much we want to finish it (the ALM season) strongly."
The reduction in Asian commitments may help Sterjovski's side refine their focus towards the back end of the season after giving Bangkok a gift with a little over a minute played.
Al-Ghassani was given all the time and space to shoot from the edge of the Macarthur box with an effort that sailed past Filip Kurto.
His goal should have been a warning to the Bulls but the one time they let their guard down, the striker made them pay.
A cross from Picha Autra found the attacker who fired past Kurto again, his goal awarded after a lengthy VAR check.
Scott hit back for the Bulls in the 41st minute when he was allowed to shoot from distance to leave them down 2-1 at halftime.
After having his penalty shout overturned, Sawyer poked home but his 90th-minute strike proved a mere consolation.
