The Sharks are now level with Persipura Jayapura with seven points with both teams having two games to play.
Talismanic 37-year-old midfielder Therdsak Chaiman was again the best player on the pitch, relentlessly picking apart the Indonesian defence with through-balls or keeping possession and movement with short passes.
Both sides struggled to find a rhythm early on with Persipura enjoying an equal share of the possession although they did not threaten the Chonburi goal.
Defender Suree Sukha broke the deadlock for Chonburi in the 16th minute but both sides were still tense and Anucha Kitpongsri earned a yellow card for Chonburi on the half-hour mark with a tackle from behind.
Persipura forward Boas Salossa broke away in the 32nd minute after a mistake by the Chonburi defence but his heavy first touch allowed the keeper to deflect the ball for a corner.
The Sharks doubled their lead three minutes later when Arthit Sunthornpit fired a pinpoint cross to Pipob that he volleyed in from close range.
Chonburi eased away and in the 40th minute Anucha set off on a mazy run through the penalty box, eluding two players before he was hacked from behind by Titus Bonai.
Therdsak, MVP in the inaugural AFC Champions League when playing for BEC Tero Sasana, calmly dispatched the penalty to make the scoreline 3-0 before half-time.
Pipob had two one-on-ones with the goalkeeper in added time but shot directly at the opposition custodian before attempting to chip him but instead, put the ball over the bar.
The second-half was mostly one-way traffic, but Persipura did manage to spurn a fine chance in the 50th minute when Sinthaweechai Hathairatthanakool fumbled a cross, dropping it at the feet of Yustinus Paew but he could not react quickly enough.
Nine minutes later the Black Pearls were reduced to 10 men when Ortizan Salossa received his second yellow card for a studs-up lunge at Kazuto Kushida.
Pipob and substitute Suppasek Kaikaew both missed chances before Therdsak beat the offside trap to feed Suppasek in the 71st minute, who fed in a cross that Pipob glanced home.
Defender Bio Paulin earned a consolation goal for Persipura with a towering header from a corner in the 75th minute, but Chonburi had three more excellent chances in the box that they squandered before the final whistle.
The result draws Chonburi level with the Indonesians at the top of Group F on seven points, two ahead of third-placed South China.http://www.the-afc.com/en/tournaments/clubs/afc-cup/34510-chonburi-v-persipura-jayapura