Bahrain won the match 10-0 having gone into the encounter in Manama knowing it needed to overcome a nine-goal deficit to have any chance of progressing to the next stage of the qualification campaign.
Qatar's 2-2 draw with Iran in the day's other Group E contest meant Bahrain's efforts were in vain, but FIFA confirmed the circumstances of Bahrain's emphatic win would come under scrutiny.
"Given the unusual outcome in relation to the results-expectation and head-to-head history, and in the interests of maintaining unequivocal confidence in our game, FIFA Security will conduct a routine examination of this game and its result," a FIFA statement said.
Bahrain, coached by former England manager Peter Taylor, has historically had close tussles with Indonesia, having won two, drawn two and lost two of its six meetings prior to Thursday (AEDT).
Bahrain had scored nine goals across those six meetings, while conceding seven.
Bahrain were given a helping hand when Indonesia lost goalkeeper Samsadir to a red card just two minutes into the contest. Indonesia had already been forced to field an inexperienced line-up as several senior players were barred from playing due to their involvement in the rebel Indonesian Super League.
Mohamed Tayeb and Sayed Dhiya both hit hat-tricks for the victors, with Ismael Abdullatif and Mahmood Abdulrahman adding a brace apiece.