The A-League club, in their first Champions League campaign, were beaten 2-1 by the Chinese champions at Tianhe Stadium but progressed on away goals following their 1-0 home win last week.
Tomi Juric, who scored the winner in the first leg, converted from the penalty spot in the 58th minute before Alessandro Diamanti levelled for Guangzhou three minutes later.
Brazilian striker Elkeson netted an injury-time winner for Marcello Lippi's side but it did not stop Tony Popovic's Wanderers from moving through to the final four where they will face South Korean club FC Seoul.
Former Crystal Palace and Socceroos defender Popovic said: "I feel very good and proud of my team. They have done a great job by showing resilience and fighting spirit.
"This was a very tough match for us. We travelled a long way to be here and we are exhausted. But we overcame all the difficulties and I am very proud."
Western Sydney will travel to Seoul for the first leg on September 17 before hosting the two-time finalists on October 1.
The other semi-final will be played between Saudi Arabia's Al-Hilal and the UAE's Al-Ain after they beat Al-Sadd and Al-Ittihad respectively in their quarter-finals.
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