Pep Guardiola's men had played one game fewer than their Chinese opponents - managed by World Cup winner Marcello Lippi - but could not make the extra freshness count in 40 frustrating opening minutes in Agadir.
Zeng Cheng was particularly resolute in the Guangzhou goal until France winger Franck Ribery managed to tuck away a poorly-cleared ball to inspire Bayern to greater things.
They would take a two-goal lead into the break thanks to Mario Mandzukic, who headed Thiago Alcantara's cross home in the 44th minute.
Bayern found the third goal they needed to put the result beyond doubt only two minutes after the restart as Mario Gotze completed an attacking move started by David Alaba.
The Bundesliga leaders will face either home hopefuls Raja Casablanca or Atletico Mineiro of Brazil in Marrakesh on Sunday, while the Chinese champions will face off with the loser of that semi-final for third place.