A Nikica Jelavic goal in the second half proved the difference in a match that never scaled great heights but showed that the Socceroos could compete with a top-class opponent.
Australia was compact throughout but a concern is the team's inability to threaten in front of goal, ahead of its World Cup meeting with Chile next weekend.
As expected, Ange Postecoglou selected a strong line-up with returning skipper Mile Jedinak in the heart of midfield with Ivan Franjic in at right-back, Alex Wilkinson in central defence alongside Matthew Spiranovic, Tommy Oar playing the No.10 role and Dario Vidosic's selection over Ben Halloran the only real surprise.
Mark Bresciano was a second-half substitute for the Socceroos as he searches for some much-needed match time.
Croatia started with regulars Ivan Rakitic, Ivica Olic, Vedran Corluka and Mario Mandzukic – suspended for the World Cup opener against Brazil – on the bench.
Mandzukic came on for Jelavic just after the goal and the Bayern Munich striker required treatment on his ankle late on.
The absence of Rakitic for the most part hurt Croatia, which, like the Socceroos, lacked the cutting edge to threaten often.
In the opening stages the green and gold looked the better of the two sides but as the first half progressed Croatia got into the game although neither side produced any notable openings in the final third.
Croatia came closest in the 20th minute as Eduardo, having been floored and requiring treatment moments earlier, forced Mat Ryan into a save down low to his right after a Jelavic cutback.
In a major worry for Croatia coach Niko Kovac, left-back Danijel Pranjic came off in the first half after twisting his ankle under a challenge.
Not much changed after the breakalthough Croatia goalkeeper Stipe Pletikosa was involved for the first time 90 seconds after the interval, easily claiming a Tim Cahill header.
Croatia captain Darijo Srna came close with a free-kick in the 56th minute, but he curled a powerful 20-yard effort wide of Ryan's goal.
Two minutes later, a lapse in the Australian defence gave Jelavic a clear sight on goal, which he duly dispatched.
The ball fell to Luka Modric on the edge of the box and as Franjic lunged in to make a tackle the ball deflected to an unmarked Jelavic, as Spiranovic and co. appealed for off-side, and he fired his left-foot shot past Ryan and in off the underside of the crossbar.
Both sides rung the changes after that point including the introduction of Bresciano for Tim Cahill on 66 minutes.
Other Australian changes included James Triosi and Matt McKay on for Mark Milligan and Oar, and Adam Taggart on for Leckie on 85 minutes.
Second-half substitute Ivica Olic tested Ryan from range as the earlier introduction of Rakitic gave Kovac's men more impetus moving forward.
The Socceroos would be content with the run out as Jedinak got through 74 minutes and the combinations in defence began to bed in.