The Thai outfit took the lead against their opponents from Hong Kong when Pipob On-Mo headed home Natthaphong Samana's cross in the 19th minute.
Chonburi continued to press and almost doubled their advantage when South China goalkeeper Yapp Hung Fai denied Kazuto Kushida.
They did not have to wait long however, as Pipob's strike partner Thiago made it 2-0 36 minutes in.
After the break, Thiago was played clear through on goal by Kushida's lofted pass and with the South China defence appealing in vain for offside, he coolly rounded the keeper and slotted into the empty net to put the result beyond doubt.
The hosts saw out the remainder of the game with ease, and progress to the next round of qualifying.
Masahiro Wada's side will now travel to China to take on Beijing Guoan, in the final preliminary round before the group stage proper begins.
