The injured players are midfielder Ngo Hoang Thinh and striker Phan Van Long.
Thinh left the field on a stretcher during a friendly match against South Korea's U-23 side on Saturday.
Doctors have confirmed that Thinh has two broken ribs and will be out of action for two months.
Long has been suffering for some time with a groin injury and will not be ready to play at the SEA Games which start on June 5 and runs up until June 16.
The Games programme will feature 36 sports in 402 events and about 7000 athletes from 11 participating nations will be competing.