The Thais walked off the pitch in the 82nd minute, protesting the decision of Malaysian referee C.Ravichandran to award a penalty to the defending champions after Noh Alam Shah went down in the box under challenge from Niweat Siriwong.
They remained off the field for 15 minutes until team manager Thavatchai Sajakul intervened and convinced the team to continue playing.
Mustafic Fahruddin promptly dispatched the spot kick to hand the Thais their first defeat against Singapore in a competitive international for 30 years.
Chanvit showed up for the post-match press conference but remained for only 10 seconds, saying: "Our comment today is that we have no comment. You can see everything that happened on the field, so we have no comment today."
Team manager Thavatchai later said that he would be lodging a protest with the Asean Football Federation, declaring that the incident had not been instigated by his own team.
Local organising committee chairman Mohammed Muzzammil said that the AFF will be investigating the matter before commenting further.
"We will wait for the match commissioner to submit his report," he said. "The AFF will then discuss the matter before determining if any further action should be taken."
While the Thais were up in arms over Ravichandran's decision, Singapore coach Radojko Avramovic felt that his side deserved the victory on merit.
"A win is a win and I felt that we fully deserved our victory tonight," said the Serbian.
"We got a great first goal from Noh Alam Shah and the penalty I felt was a punishment for the Thais because they were using their hands all the time during the game.
"I didn't see the incident clearly but they were using their hands all the time to pull back our players. There was even an incident earlier in the second half when Alam Shah was pulled back which should have been a penalty.
"But I felt that our players did really well tonight. Congratulations to them and the people who came out to support us."
Avramovic was far from pleased with the Thai reaction to the penalty decision.
"I think it was a joke," he said. "I just told my players to keep their focus and keep themselves ready because I felt sure they would come back."
A fiery atmosphere can be expected from the Thai fans in Bangkok on Sunday evening when Singapore will look to defend their lead in the second leg but Avramovic does not believe that the situation will get to his charges.
"I think for me, this is sport and there are 11 players on each side who will play the game. Whatever happens on the terrace is something for somebody else to control," he said.
"Our players have already played a few games in those sorts of surrounding so I don't expect that it will be a big thing for them."