Andrija Kaluderovic netted the only goal for the Hyundai A-League side against his former team, as Frans Thijssen’s men, still third in Group G, moved to seven points.
Beijing and Suwon Bluewings are joint top on 10 points, both with a superior goal difference to the Australian side.
For the The Roar to have any chance of going through they must beat the Reds well at home in their final games and hope for a similar result in the other game.
The first-half at the Workers’ Stadium in Beijing had a lot of attacking options but very few decent chances.
The home side had a chance to score in the eighth minute when Erton Fejzullahu headed wide from Li Yunqiu’s cross.
In the 17th minute Brisbane had a chance when Devante Clut hammered a shot at goal that went wide.
In the 40th minute the visitors scored when Matt McKay picked out Clut in a good area and the 19-year-old flicked a brilliant first-time pass into the path of Kaluderovic, who was left with a relatively simple finish past goalkeeper Yang Zhi.
The visitors nearly doubled their lead in the 51st minute when Borrello hammered his shot wide but should have passed rather than shoot as Kaluderovic was in a far better position on his left.
The hosts nearly scored in the 60th minute when goalkeeper Jamie Young saved a Pablo Batalla free-kick that was heading towards the top corner.
Guoan kept up the pressure trying to score but were denied by good defending and in the end The Roar gave the Chinese side their first home defeat since August 2014.