A section of the home support attack visiting Vietnam fans after Thailand went 2-1 down in Sunday's encounter.
The violence has been widely condemned, and police have acted swiftly to bring those responsible to book.
While the police continue their investigation, Malaysia's sports minister Khairy Jamaluddin apologised for the incident.
"I saw with my own eyes, the Vietnamese supporters were assaulted by a group of Malaysian fans at Shah Alam stadium," commented .
"There is no excuse for this violent behaviour. These violent fans do not represent Malaysia. My sincere apologies on behalf of Malaysia for the actions of these small number of irresponsible thugs."