It's a result they'll probably take in the circumstances with a raft of key players missing. They had to rely on a string of strong saves from Jamie Young on Tuesday night to keep the Thai Premier League champions at bay.
Skipper Matt McKay (broken nose), Thomas Kristensen (hamstring) and Luke DeVere were all ruled out as coach John Aloisi called on a number of youth players to scrape together a team for the Roar's sixth match in 22 days.
Striker Jamie Maclaren and veteran playmaker Thomas Broich both came off the bench in the second half but neither could find the breakthrough Brisbane needed in front of just 4536 supporters.
The Roar were warm favourites to win but it was never going to be an easy task against Muangthong - six of their starting players featured for Thailand in November's 2-2 World Cup qualifying draw against the Socceroos.
Brisbane were heavy-legged after Saturday's A-League clash away with Perth.
The visitors generated the better chances on goal - and had 16 shots to Brisbane's seven - but simply could not get past goalkeeper Young, who Aloisi had rested from A-League duties to keep him fresh for the ACL.
Former La Liga striker Xisco - who transferred late last year to the Thai club - was a constant threat up front for Muangthong but Young, stand-in captain Jade North and his rookie defensive partner Cameron Crestani thwarted him and his teammates at every turn.
Crestani, making just his second senior appearance, was particularly impressive and made several key clearances and interventions.
Nick D'Agostino came closest to scoring for the Roar just before halftime, when the 18-year-old latched onto a cross from fellow teenager Dane Ingham, who was playing just for the third time at senior level and out of position at left-back.
However, Muangthong gloveman Kawin Thamsatchanan managed to get a hand on D'Agostino's attempt before it cannoned into the post and then out for a corner.
Kashima Antlers won 2-0 in Group E's other match against Ulsan Hyundai, who the Roar will take on next Tuesday night in South Korea.