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South China – who sit second in the Hong Kong top flight – entered their trip to Tampines Rovers in Singapore on the back of a 12-match unbeaten streak.
And they took the lead after 21 minutes when Australian Andrew Barisic converted Lee Wai Lim's assist.
Mrdakovic's goal forced extra time, but Barisic was again on the spot for Po Chuen Cheung's side, striking in the 103rd minute to secure South China's place in the second round of qualifying.
South China will visit Thailand's Chonburi in the next phase of the competition.
Other results on Sunday saw Akarandut Orok net twice in extra time for Bahrain's Al Hadd, who won 3-1 at Shabab Al Ordon in Jordan, while Brahima Keita's stoppage-time strike gave Kuwait outfit Al Qadsia a 1-0 win at Al Suwaiq in Oman.
