The Socceroos will be forced into at least two injury-enforced changes with defender Jacob Italiano (adductor) joining Mathew Leckie on the sidelines.
But all eyes will be on how Australia's attack shapes up for a clash with plenty on the line.
With a win or draw at Levi's Stadium in Santa Clara on Thursday (Friday AEST), Australia will finish second in group D, and face the Group G runners-up - one of Belgium, Egypt, Iran or New Zealand - in Dallas.
A defeat would mean a nervous wait, but probably still progression as one of the eight best third-placed teams - and a likely clash with Group E winner Germany in Boston.
Wednesday's results didn't materially affect Australia's hopes of progression.
Fall-out from the 2-0 defeat to the US centred on Popovic's decision to drop goalscorers Irankunda and Connor Metcalfe for Nishan Velupillay and Leckie.
Irankunda, Metcalfe and Cristian Volpato all eventually impressed when brought off the bench.
"Whoever starts tomorrow, I know can build a strong foundation, and whoever comes on can finish what we've started," Popovic said.
Popovic said he wouldn't in hindsight change the line-up he'd chosen against the US - just their first-half performance.
He added: "But I'm sure from that experience we'll be better against Paraguay and, God willing, we get through, we'll be better again for the next experience and Nestory plays a big part in that, of course."
Veteran attacker Leckie (hamstring) limped off against the US.
Popovic confirmed right wing-back Italiano had been injured in training and would have further scans to determine its severity.
Losing Italiano, who started against Turkey and the US, is a blow.
With Lewis Miller (Achilles) sidelined months ago, Italiano is the only specialist right wing-back, marshalling the opposite flank to Jordan Bos, in Australia's squad.
Jason Geria, left-back Aziz Behich and Kai Trewin are Italiano's potential replacements.
Popovic was effusive in his praise for how his players had been "growing day by day" on the World Cup stage and their response to a disappointing first half against the US.
"These young boys are learning on the go. It's very quick education and lessons that we are learning," he said.
"I'm seeing them grow as young men, I'm seeing them grow as players, I'm seeing them mature.
"I'm seeing them enjoying and embracing the greatest challenge of all, which is the World Cup. It doesn't get greater than this."
Defenders Harry Souttar, Alessandro Circati and Bos are all carrying yellow cards, which means a booking would result in suspension for the round of 32.
"It's not something that I need to focus on - I'll think about that after the game," Circati said.
"Obviously, you need to play keeping yourself a bit aware of that.
"But you can't let that affect your match, because I'd rather go past the round and get a yellow card than not pass at all."
The Socceroos have won just nine of 50 matches against South American opposition.
Circati plays with several South Americans at club level and expects a tough test.
"They don't back down to anyone, but neither do we," he said.
Popovic hailed resilient Paraguay and their coach Gustavo Alfaro, who told media his team would play like there was no tomorrow.
"We know nothing's given to you at a World Cup, we'll have to earn everything tomorrow night," Popovic said.
"We expect that, we actually want that. That's how it should be, and we're looking forward to a great test."
