Both Thai clubs have home ties for the last 16 as a reward for finishing top of their qualifying group.
Muang Thong United are at home to Al Ahed (Lebanon) while Chonburi will entertain Sriwijaya (Indonesia).
The rest of the draw is:
Nasaf (UZB) v Al Faisaly (JOR)
Duhok (IRQ) v Dempo (IND)
Arbil (IRQ) v Tampines Rovers (SIN)
Al Qadsia (KUW) v Kuwait SC (KUW)
Al Wehdat (JOR) v Shurtan (UZB)
Song Lam Nghe An (VIE) Persipura Jayapura (IDN)
Ties will be played on the 24th and 25th May.