The winner came only moments after being reduced to 10 men.
Atletico took the lead just two minutes into the contest through Diego Tardelli but then saw Guangzhou score twice in the space of seven minutes to turn it around before 15 minutes had been played.
Muriqui equalised in the ninth minute before Dario Conca had them ahead from the penalty spot.
Ronaldinho levelled the game once more in first-half stoppage time, but he would be sent off in the 87th minute for a stamp on Zhao Xuri and stoppage time was looming before Luan found the net at the death.
The match was the last in charge for Atletico coach Cuca, who is to take over at Shandong Luneng in China.
Conca was also appearing in his final game for Guangzhou before moving to Fluminense in Brazil.