Automatic qualification for the 2018 World Cup is guaranteed by finishing in either of those two spots, with Japan and Saudi Arabia now three points ahead of Australia.
Sara Zelenak, 21, from Brisbane and the South Australian Kirsty Boden, 28, were killed in Saturday night's terrorist attack.
According to News.com in Australia, the pregame moment of silence itself was approved by both Asian Football Confederation officials and the Saudi team, but a spokesman for Football Federation Australia said the Saudis also informed game officials that they would not be taking part.
These teams have only met on Australian soil once before in a competitive match, back in 2012, when Australia won 4-2 in Melbourne, a result considered a $46 chance to be repeated on Thursday.
After a home game against the Saudis on Thursday, Australia will play a friendly against Brazil to prepare for the Confederations Cup in Russian Federation.
Saudi Arabia's players did not line up for the minute's silence against Australia. Zelenak was working in London as a nanny and Boden was a nurse, whose family said she died running "towards danger, in an effort to help people on the bridge".
"Tom brings absolute class, he's comfortable under pressure and in the heat of battle we all play at 100 miles an hour, but if you want to take the steam out of the game and add some class, he's your man".
The game, which was a World Cup qualifying match for the 2018 World Cup in Russian Federation, saw Australia beat the Saudis 3-2.
Australia remain third in Asia's group B but join leading Japan and the second-placed Saudis on 16 points.
But the crowd did not ignore it and roared with delight as striker Tomi Juric scored a first-half brace, twice giving the Socceroos the lead.