The mauling in Manama raised suspicion because Bahrain needed a huge turnaround to have any chance of reaching the fourth round of regional 2014 qualifiers.
Bahrain had to beat Indonesia, hope Qatar lost to Iran and also make up a nine-goal difference on the 2022 World Cup hosts.
FIFA's security department has launched a routine probe, which the AFC said on Friday it supported and would "cooperate closely with."
"I have read the media reports about suspicions of match-fixing," he said. "But I am confident that none of our teams are involved in this. Bahrain were the better team both tactically and technically.
"Moreover I have gone through the official reports of the AFC match commissioner and the match referee and they indicate nothing."
"It has to be taken very seriously regardless of what region it is played in. It is a world issue, not just simply in the Asian region," he told Reuters in London.
"We need to put as much resources as we can into this aspect of football and support those who are dealing with it in FIFA.
"The important thing is that if there are suspicions you have to investigate it.
"It might just be a coincidence, however there might be something behind it. Regardless, it can happen in any country in the world."
Bahrain's 10-goal rout almost sent them through but Qatar advanced after an 86th-minute goal gave them a 2-2 draw and the point they needed in Tehran to clinch second place in Group E.
Indonesia, already eliminated, fielded a inexperienced side of mostly uncapped under-23 players after they were blocked by the country's federation from selecting their regular squad because they mostly play in the breakaway Indonesian Super League.
"We apologise to the people of Indonesia," Indonesian Football Association (PSSI) secretary general Tri Goestoro said in a statement.
"The PSSI tried to pick the best players and aimed for the best results for the last match. But Bahrain was clearly playing better and defeated us."
