Chonburi went ahead after 19 minutes when Natthaphong Samana set up Pipob On-mo. More chances followed but South China keeper Yapp Hung Fai kept his side in touch.
However, Brazilian striker Thiago Cunha eventually doubled Chonburi's lead in the 36th minute.
Cunha struck again after half-time to put Chonburi 3-0 ahead, beating an offside trap and scoring from close range.
Chonburi will face China's Beijing Guoan on Feb 15 for a place in the group stage.