Myanmar, who hosted Group B, edged Malaysia 1-0 while Vietnam beat Cambodia 2-1 in their final matches on Saturday night.
Vietnam finished first in Group B with three wins, ahead of Myanmar who had six points.
Thailand, as Group A champions, will travel to Myanmar in the first leg on Dec 4 and are at home in the return leg on Dec 8.
Thailand coach Kiatisak Senamuang wanted to flaunt the depth of his team and he succeeded in his mission as a second-string Thailand side showed the Philippines the Suzuki Cup exit, inflicting a 1-0 win in Manila on Friday night (Nov 25).
While Thailand ended their Group A campaign with a perfect nine points from three wins in as many matches, the hosts failed to make it to the last four.
Midfielder Sarawut Masuk scored the winning goal for the Kingdom as the defending champions reasserted their status as the hot favourites for this year’s Southeast Asian title.
Kiatisak decided to rest star playmaker Chanathip ‘Messi Jay’ Songkrasin, first-choice goalkeeper Kawin Thamsatchanan and prolific striker Teerasil Dangda for the match.
The event also ended in disappointment for Singapore, who were hoping to go all the way and claim their fifth Southeast Asian crown.
Both Thailand and Singapore have won the tournament four times each.
Indonesia celebrated their return to international football after a Fifa-imposed two-year suspension with a place in the semi-finals of the Suzuki Cup following an impressive 2-1 victory over Singapore, also on Friday night.
Kiatisak said: “I’d like to praise my players for following the game plan and helping us grab three points from the match and nine points from the first round.
“We have shown that all the 23 players that we called for this tournament have equal potential.
“The hosts wanted to win the game and they did make things tough for us.
“We have to continue to work hard for the semi-finals. We are taking things step by step and this has been the first step for the team with the semi-finals being the second and the final the third.
“We had three games in the first round which made us face varying situations and different challenges.
“I reconfirm that we will try to defend the title for His Majesty the King [who passed away last month].”
However, Kiatisak has warned his men to stay fit or be ready to get punished by Myanmar in the two-leg 2016 Suzuki Cup semi-final.
Kiatisak said he was expecting two tough games against a “fit and strong” Myanmar side.
“The away game is likely to be a tough one.
“This Myanmar team is good. They have a good mixture of veterans and players from their youth team which reached the Fifa U20 World Championship last year.
“They have good speed when attacking from both wings and striker Aung Thu, who is just 20, is also quite good.
“We cannot underestimate them at all and they will have a big support from the local crowd in the first leg which can inspire them to do something special.”
Kiatisak insisted that fitness will be the key to winning the semi-final battles.
“We must prepare ourselves well and our fitness must be very good. Our mission is not yet finished.
“If we are not fit, we may get punished by Myanmar. They just showed us what they they are capable of when they beat Malaysia,” Kiatisak said.
The biennial Suzuki Cup is considered the Southeast Asian championship.