The Chelsea winger, three minutes after hitting the bar, feigned a shot before cutting past two defenders to score in the 62nd minute and settle a match his team dominated while rarely threatening to break through.
Belgium, with Manchester City defender Vincent Kompany back after a two-month injury layoff, were on top from the start.
The hosts, however, struggled to penetrate Macedonia's well-organised defence and lone striker Christian Benteke was a peripheral figure.
Belgium won corner after corner but did not force a single save from keeper Tome Pacovski in the first half although Thomas Vermaelen had the ball in the net in the 34th minute only to be adjudged offside.
Macedonia came more into it after Hazard's goal without looking likely to score.
Highly-fancied Belgium, packed with English Premier League talent, have 16 points from six matches, the same as Croatia but ahead on goal difference.
- Sports & Recreation