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.
Rovers were reduced to 10 men in the 33rd minute when Imran Sahib was sent off, but Serbian Miljan Mrdakovic levelled proceedings 19 minutes into the second half.
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.
To make matters worse for Rovers, Mrdakovic was dismissed for a second yellow card with six minutes to play.
South China will visit Thailand's Chonburi in the next phase of the competition.
Al Kuwait made it five competitive wins in a row with a 1-0 success over Al Shorta of Iraq.
Javad Nekounam scored the only goal of the game in the 63rd minute for Al Kuwait, who will travel to Uzbekistan to meet Lokomotiv in the second round of qualifying.
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.
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