Australia posted a 2-1 win over Thailand on Tuesday night in Melbourne while Saudia Arabia beat Japan 1-0 hours later to seal their automatic qualification spot and force the Socceroos into the play-off round.
Japan had already booked their place in Russia sitting top of Group B, while South Korea joined table-toppers Iran in progressing from Group A.
Syria continued their remarkable underdog story with a last-minute equaliser against Iran in Tehran – Omar Al Soma's strike booking a play-off encounter against Australia, with Uzbekistan shunted into fourth place on goal difference.
Australia and Syria are set to face each other over two legs next month, with the winner going on to face the fourth-placed side from the CONCACAF section in November with a World Cup place on the line.
The AFC made no mention of any specific allegation in a statement released on Wednesday (Thursday AEST) but noted its members had recently been reminded of their obligations under the "principle of political neutrality".
"The Asian Football Confederation has begun investigations following reports of breaches of regulations at the FIFA World Cup 2018 Asian final round qualifying matches played on September 5, 2017.
"The AFC is currently waiting to receive all relevant reports before proceeding with the next steps. The AFC will also co-operate with the world governing body, FIFA, to provide the necessary reports on matters which fall within the jurisdiction of FIFA.
"In June, the AFC wrote to its member associations reiterating that all stakeholders involved in Asian football must respect the principle of political neutrality."