The Socceroos couldn't build on last week's impressive 2-2 draw against world champion Germany in Kaiserslautern, creating little in attack against the world's 108th-ranked side.
Both teams lacked fluency on a choppy pitch at Phillip II Arena, with just a few thousand fans turning up to watch the underwhelming international.
Among the positives for Socceroos coach Ange Postecoglou was a strong game from in-form Melbourne City midfielder Aaron Mooy, who started in one of six changes from the draw against Germany.
Right-back Tarek Elrich earned a first international cap, while teenager Chris Ikonomidis came off the bench late to become the first player since 1981 to make his Socceroos debut before playing a senior club game.
AFC Asian Cup hero Massimo Luongo, Trent Sainsbury, Adam Federici and Aziz Behich all came into the starting line-up and the changes looked to take some wind out of the Socceroos' sails although Australia dominated possession in the first half.
A 30th-minute Nathan Burns effort was the the visitor's sole shot on target and it lacked the attacking fluency that caused Germany so many problems.
Macedonia looked dangerous on the counter attack, with Elrich forced to make a crucial header to stop the home side's best attacking move in the 16th minute.
Mile Jedinak earned a booking just before halftime for a challenge that resulted in Dushko Trajovski being stretchered off the field.
The second half was equally scrappy, though Macedonia caused the Socceroos problems with its pace in transition.
Luongo grew into the game and Leckie threatened in attack but was let down by his finishing on several occasions, including a free header from a dangerous Burns cross in the 56th minute.
Australia went agonisngly close to taking the lead on 66 minutes as a Leckie cross-goal shot was saved by goalkeeper Besart Abdurahimi. Substitute Tomi Juric was unable to force in the rebound.
Bailey Wright, Tommy Oar, Oliver Bozanic and Mitch Langerak all saw game time in the second half, with 19 year-old Lazio reserves winger Ikonomidis looking lively after coming on with eight minutes to play.
The match was Australia's final hit-out before 2018 FIFA World Cup qualifying begins in June.
Socceroos line-up: 18. Adam Federici (gk) (12. Mitch Langerak (gk) 62’), 7. Mathew Leckie, 8. Aaron Mooy (9. Tomi Juric 62’), 13. Aziz Behich, 14. James Troisi (11. Tommy Oar 46’), 15. Mile Jedinak (10. Oliver Bozanic 72’), 16. Nathan Burns (25. Chris Ikonomidis 82’), 19. Tarek Elrich, 20. Trent Sainsbury (6. Bailey Wright 46’), 21. Massimo Luongo, 22. Alex Wilkinson.
Unused Substitutes: 1. Mat Ryan (gk), 2. Ivan Franjic, 3. Jason Davidson, 17. Matt McKay, 24. Luke DeVere
