Midfielder Stephan Schrock's 51st minute goal off a corner was the difference-maker at PAT Stadium, as the visitors grabbed control of the match early in the second half and never looked back.
The result came a week after Schrock and co. survived a thrilling 3-2 victory over Myanmar's Shan United in in Manila.
With the win, the Busmen advance to the playoff round against Japan's FC Tokyo. The two sides meet at Ajinomoto Stadium in Tokyo on January 28.
The winner of that match secures a spot in Group F of the AFC Champions League group stage, alongside South Korea's Ulsan Hyundai, China's Shanghai Shenhua, and Australia's Perth Glory.
A win for Ceres Negros will prove to be historic, as it would make it the first Filipino club to participate in the regional club competition.
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