"I thought today also we played much better than our opponent and they shot two times and they were very lucky," he said.
"We have a problem at this level to score a goal.
"They did everything I asked. We played football very well. We got a lot of chances only we cannot score."
The Socceroos were all over Peru in the opening 20 minutes, pressing forward deep into opposition territory at will. Tomi Juric found space inside the box but couldn't find a teammate with a ball across the face and a Robbie Kruse cross was cleared away.
But the men in gold were blindsided by a piece of individual brilliance that gave Peru the lead. Captain Guerrero latched onto a long ball then chipped to Andre Carrillo inside the box, who thumped a stunning volley across the body of Mat Ryan and into the back of the net.
There were suggestions Guerrero may have been offside, but the decision was not reviewed with VAR. Van Marwijk was in no doubt Guerrero was offside.
"The first goal was offside," he complained. "They shot one time on the goal and it was offside. I saw it on the video."
Defender Trent Sainsbury — who was marking Guerrero and got a boot to the ball before it bounced in front of the Peruvian captain's path — echoed his coach's thoughts. "I feel it should have been offside. If he wasn't there and I knew he was offside, I wouldn't play the ball," he said.
Peru had failed to score in its first two games against Denmark and France despite taking 27 shots — but it only needed one effort on goal to break the drought against the Aussies.
The Socceroos continued to dominate the half without reward. Tom Rogic — who was Australia's best with the ball before he was substituted late in the second half — showed brilliant close control to dance his way past defenders inside the box and let loose with a left-footed strike.
Twice Robbie Kruse found space down the left before crossing inside to Mathew Leckie — but both times Leckie was unable to convert, even accounting for the linesman raising his flag for offside on the first attacking raid when a heavy first touch gave the Peruvian defence enough time to close him down.
Leckie's second foiled opportunity — when two defenders lunged desperately to block him from close range — was symptomatic of Australia's day.
The second half started in the worst possible fashion for captain Mile Jedinak and Co.
A deflected shot inside the box bobbled away and Guerrero was quickest to react, sweating on the bouncing ball and hitting it first time with his left foot. That strike hit Mark Milligan and the latest deflection gave Ryan no chance.
"It's a killer blow for the Socceroos," SBS commentator David Basheer said. "It's a cruel twist for Mat Ryan, who's been quite superb in this World Cup."
That prompted the introduction of Cahill and Arzani, who both added spark. A defender got in the way of Cahill's first shot on goal before Arzani tried his luck from long range with a shot that sailed over the bar.
Aziz Behich missed a golden chance to set up Cahill for Australia's first goal. With 20 minutes to go he latched onto a dinky aerial ball on the left edge of the box and tried to volley it across the face of goal, where an unmarked Cahill had drifted into space. But Behich miscued his pass and it missed his 38-year-old teammate by several metres.
Peru narrowly missed a chance to add a third goal to its tally Flores hit the post in the 80th minute — but the linesman's flag was up for offside.
