In a match of very few clear-cut chances in Skopje, the Socceroos were the better side but lacked the same cutting edge they showed in an impressive 2-2 draw with world champions Germany last week.
Australia missed the energy and quality they showed in Kaiserslautern - especially in midfield - with the home side making it hard by sitting deep.
After a scrappy start, it was Ange Postecoglou's men who created the first real chance on 12 minutes.
Mathew Leckie found Nathan Burns on the right and the Wellington Phoenix man burst into the box and found James Troisi, but his snap shot took was deflected wide of goal.
Australia goalkeeper Federici was not tested in the first half, while opposite number Martin Bogatinov was only called on once to deny Burns on the half-hour mark.
After winning a free-kick on the left, Burns picked himself up to get the ball short before turning past a couple of defenders and surging into the box, only to shoot straight at Bogatinov.
The second half started in a similar vein to the first, with the Socceroos enjoying most of the possession and trying to unlock Macedonia's compact defence.
Leckie almost did that 12 minutes after the break, getting on the end of Burns' cross, but his far-post header sailed just over the bar.
The FC Ingolstadt man went even closer midway through the half, turning brilliantly on Aziz Behich's ball into the box, with Leckie's powerful low drive forcing substitute keeper Kristijan Naumovski into a smart save.
With nine minutes to go, impressive teenager Chris Ikonomidis was brought on for his international debut, but not even the Lazio winger's youthful exuberance could spring the contest to life late on as both sides were seemingly content to play out a bore draw.
