Chiangrai claimed the lead through Lee Yong-rae but the visitors equalised with less than 10 minutes left in the first half.
Suriya Singmui, however, ensured the hosts went into the half-time break ahead, before Rosimar Amancio scored the final goal of the night three minutes from full-time.
Neri Caldeira Junior’s side will take on Japan's Sanfrecce Hiroshima in the playoff next Tuesday.
Chiangrai, the 2018 Thai FA Cup winners, had the lion’s share of possession in the opening minutes, and were successful in translating it into an opening goal in the 12th minute with Lee finding the back of the net.
The former Suwon Samsung Bluewings midfielder could have doubled Chiangrai's tally in the 27th minute with a free-kick but shot straight into the Yangon wall.
Yangon, who had defeated Philippines champions Ceres Negros in the first preliminary round, drew level in the 36th minute through Pyae Phyo Zaw in the 36th minute but it was short lived as Singmui restored Chiangrai’s lead two minutes later to make it 2-1 before the break.
Despite having the advantage, Chiangrai went in search of their third goal and brought on Chaiyawat Buran and William Henrique in the 52nd and 62nd minutes but the five-time Myanmar National League champions showed their defensive resolve.
Yangon made three changes of their own but it was not to be as Chiangrai’s Amancio sealed their convincing win in the 86th minute.
In Pathum Thani, Hanoi FC’s Nguyen Van Quyet beat Bangkok United 1-0.