Goals from Mark Bridge and Tomi Juric on a rain-sodden surface at the Tianhe Stadium were not quite enough as FC Seoul beat Kashima Antlers 3-2 with a last-gasp goal in the other group match to pip Tony Popovic's men for second place and qulification for the knock-out stages.
With only a win good enough to give them any chance of staying in the competition, the Wanderers - who finished with eight points from their six group games - came out full of intent on a surface better suited to waterpolo than football against already qualified Evergrande.
And they had a shout for a 20th minute penalty when Rong Hao barged over Juric, who may have been playing his final game for the club, in the box. But the striker's pleas for a spot-kick went unanswered.
At the other end, the group winner also looked menacing with Yu Hanchao volleying over in the 29th minute as the Wanderers were forced to retreat.
The goal the defending champion craved came in the 33rd minute when a dreadful lapse from Guangzhou defender Kim Young-gwon left space for Bridge to run into and he brushed past one challenge before executing a composed finish to give Tony Popovic's men a surprise lead.
Iacopo La Rocca came close to adding a second in the 49th minute with a thunderous drive which brought a flying tipover save from Li Shuai.
Keeper Ante Covic came to the rescue for the Wanderers in the 57th minute as he raced from his line to deny Li Xuepeng as he closed in on goal.
Juric pounced with a rasping shot in stoppage time to boost his own stocks as he seeks a move elsewhere - but it was not enough to see the Wanderers through.