Macedonia started the match quicker than Wales and their early dominance was almost rewarded, but Trifun Kostovski was just unable to get his toe to Darko Tasevski's low cross.
However, the hosts eventually took the lead on 20 minutes when Goran Pandev's free kick struck the wall and rebounded kindly for Trickovski, who calmly fired the ball low into the bottom corner of the net.
The visitors, who left Real Madrid star Gareth Bale on the bench for the entire match, improved after falling behind.
Craig Bellamy struck the post with a free kick midway through the opening half, before a clever piece of skill from Ramsey drew a foul out of goalscorer Trickovski, allowing the Arsenal midfielder the opportunity to score from the resultant spot kick.
Ramsey and Joe Ledley spurned chances to put Wales ahead after half time, and that wastefulness was punished late on as Trajkovski drilled home from 20 yards following a mistake from David Vaughan.