The victory, coupled with BEC Tero Sasana’s surprise 1-1 draw at Police United, sent the Kirins to the top of the table.
After 13 matches, Muang Thong have 27 points and BEC Tero 25.
At Thammasat Stadium, French striker Michael Murcy stunned BEC after 35 minutes and Japanese midfielder Sho Shimoji equalised for the Fire Dragons in the 68th minute.
BEC threw everything at Police in the closing stages but failed to score a winner.
At SCG Stadium, Thailand striker Teerasil Dangda returned from injury to help the Kirins edge past Chonburi.
Teerasil tormented Chonburi’s defence throughout the match, setting up the winner and earning a penalty.
Mario Gjurovski scored the winning goal in the 37th minute thanks to a pass from Teerasil.
Muang Thong were awarded a penalty in the second half after Teerasil was tripped by Anderson dos Santos. However, Gjurovski missed from the spot as his shot was saved by in-form goalkeeper Sinthaweechai Hathairattanakool.
At Si Sa Ket, Suphanburi returned to form with a 5-1 win over Si Sa Ket.
Suphanburi got goals from Luis Fernandes (21), Bjorn Lindemann (55 and 59), Jakkraphan Pornsai (62) and Diouf Bireme (80) while Santirat Wienginn scored a consolation goal for the hosts in the 65th minute.
Suphanburi have had an inconsistent season with wins over top teams such as Muang Thong and losses to lowly sides.
At PAT Stadium, Air Force defeated hosts Singhtarua 2-1 for their first win of the season in a match between two former powerhouses.
Singhtarua’s Hironori Saruta opened the scoring after 39 minutes only for Sarawut Kanyanabundit and Hermann Kouassi to hit back in the second half.
At Thai-Japan Stadium, Bangkok United drew 0-0 with Chiang Rai United in a lacklustre match.