Craig Levein's side, who drew 0-0 with Serbia in Group A on Saturday, were booed off by the Tartan Army after they were forced to come from behind to rescue the draw.
Macedonia stunned the home crowd when they took an 11th-minute lead through Nikolce Noveski, although the defender appeared a yard offside when he converted Ivan Trickovski's centre.
The visitors almost doubled their lead when Goran Pandev played in Agim Ibraimi but Allan McGregor pulled off a fine save in the home goal.
Andy Webster headed over and Shaun Maloney's free-kick was punched away by Martin Bogatinov as Scotland rallied and they netted the equaliser two minutes before the break.
Jamie Mackie beat the offside trap and unselfishly rolled the ball to Kenny Miller to side-foot home from eight yards out.
Paul Dixon's low long-range effort was gathered by Bogatinov after the restart, while McGregor was forced to block Daniel Georgievski's shot shortly before Ferham Hasani rattled the post from 18 yards.
Jordan Rhodes was introduced off the bench to loud cheers in the 66th minute and he went close just two minutes later as he headed Charlie Adam's cross into the side-netting.
Scotland were indebted to McGregor once again when he denied Mirko Ivanovski with his legs and they were unable to find a late winner as Macedonia shut up shop.
Support the USA national team with an official 2013 Centennial soccer jersey from Nike. Its Official.
The hoop soccer jersey is classic and cool. The USA hooped jersey is perfect for every fan. Get in the Gear.
Jamaica is in need of a win against the U.S. Get the jersey of the Reggae Boyz.
Germany is one of the top teams ever and they will play the US on Sunday.
The adidas Nitrocharge is the most talked about new cleat in years. It was released on May 15 and will take your pitch by storm.
Neymar's move from Santos to Barcelona is no doubt the biggest summer transfer.
England will debut their new away jersey against Brazil at the Maracana Stadium on Sunday. Get in the Gear
Manchester City will try and win back the Premier League title with this new soccer jersey from Nike!
The Nike Hypervenom is the latest cleat silo from Nike. It will change your game and is worn by the game's top players.
The USA will wear their blue away jersey against Jamaica in their World Cup qualifier on Friday night.