Van Marwijk's team were again made to pay for their lack of a cutting edge and succumbed to goals from Andre Carrillo and Paolo Guerrero for the already-eliminated South Americans in this group finale.
They go home without a win, joining Peru in being eliminated in Group C as France and Denmark -- who drew 0-0 in Moscow -- both go through. Indeed, that result confirmed that even an Australian win here would have been in vain.
For the Socceroos it is a third consecutive World Cup in which they have failed to make it beyond the group stage since making the last 16 in 2006.
Van Marwijk's team took just one point, against the Danes, in between a narrow defeat against France and then this reverse.
"Not a success but also not a failure," was how Van Marwijk described the campaign in Russia. "I think everybody saw the way we performed and played. We have got a lot of compliments, but with compliments you don't win games."
Australia's only goals in Russia have come from two Mile Jedinak penalties. Against Peru they enjoyed much of the possession, with Aaron Mooy prominent in midfield, but there was no cutting edge.
Cahill finally appears
Even the introduction of veteran forward Tim Cahill from the bench made no difference.
The 38-year-old replaced Tomi Juric up front early in the second half for his first appearance of the tournament. But there was to be no goal that would have seen him join the likes of Pele and Cristiano Ronaldo in scoring at four different World Cups.
"In all three games we couldn't really make the difference in goals, and that is something this squad misses on this level," admitted Van Marwijk, who now makes way for incoming coach Graham Arnold.
Elation for Peru
For Peru there was only elation at ending their long wait for a victory in the competition, after nine attempts since defeating Iran 4-1 in 1978.
They will now hope to build on their performances in Russia after finally coming in from the World Cup wilderness.
Their vast travelling support, clad in white and red, made up the majority of the 44,073 crowd on Russia's Black Sea coast.
The stadium erupted when Watford winger Carrillo volleyed in the 18th-minute opener from a Guerrero assist for Peru's first World Cup goal since Guillermo La Rosa 36 years ago.
Australia appealed in vain for offside, but they had chances to equalise after that, with the best coming when Tom Rogic, the languid Celtic playmaker, dribbled into the area before seeing his shot saved by Pedro Gallese.
However, their hopes of turning the tide in the second half were dealt a hammer blow five minutes after the break as Peru increased their advantage, Christian Cueva setting up Guerrero to hook a shot beyond Mathew Ryan in goal.
After only being cleared to play in this World Cup at the last minute following a long legal battle against a doping ban, the moment was particularly sweet for Peru's veteran captain.
If the final score was a painful one for Australia, it was hard to begrudge the Peruvians this win, especially their army of supporters who have lit up the tournament and will be missed.
"Congratulations to the players for the great effort they put in and to the crowds who accompanied us. At least we managed to get a victory for them and for the people back home," said Peru coach Ricardo Gareca, whose future in charge is now up in the air.