An 87th-minute goal from Honduran forward Georgie Welcome gave Jose Alves' men the points after they had levelled matters 12 minutes earlier through Daiki Iwamasa.
That win moved BEC to the summit of the division after Muang Thong were hammered 5-2 at home by Suphanburi, who benefited from a Bjorn Lindemann double before being reduced to 10 men late on.
Songkhla United beat Police United 4-2 in a battle of two sides near the bottom of the division, a double from Adnan Barakat helping settling the clash in the visitors' favour.
Brazilian striker Leandro Tatu scored the only goal of the game in the 67th minute to earn all three points for Thawatchai Damrong-Ongtrakul's hosts.
Elsewhere, Chiangrai United won 1-0 at Sisaket, Osotspa drew 1-1 with PTT Rayong and TOT and Ratchaburi's encounter ended goalless.
