A Daniel Arzani strike and Tamas Kadar's late own goal, which came after Trent Sainsbury comically put through his own net, ensured the Socceroos added another morale-boosting victory to the 4-0 triumph over Czech Republic last week.
Van Marwijk was candid in his assessment of a below-par performance, claiming his squad were tired after three weeks of training and preparations for their campaign in Russia.
"It's to do with form a little bit. I think they were all tired. You could see that," Van Marwijk told Fox Sports in Budapest.
"We worked very hard the last three weeks. We gave them a rest in the last three days but, with this weather, you could see they were tired.
"I'm glad we have kept everybody fit in the training camp."
Australia had Mat Ryan to thank for keeping them in the game with a string of good saves in the first half and Van Marwijk confirmed the Brighton and Hove Albion goalkeeper would be his first choice for the World Cup.
The Dutchman also praised Tomi Juric after the striker continued his comeback from a knee injury by playing over 30 minutes as a substitute.
"I could not be satisfied about the first half but we didn't have a goal against us," said Van Marwijk.
"The second half was much better.
"Juric has done really well in the last week of training and he deserved his chance. What he showed, that's why we took him. He's done really well.
"I'm 80-90 per cent sure of my starting line-up. Ryan will be in goal."