Lewis Chalmers' penalty made it five unbeaten for Macclesfield and piled more pressure on struggling Bradford.
Chalmers netted when referee Rob Lewis awarded a controversial spot-kick after Ross Draper collided with Luke Oliver.
Macc could have had more goals but Tony Diagne fired just over and Scott Boden hit the post.
Bradford almost equalised in stoppage time but Oliver headed inches wide from eight yards and his side remain just a point clear of the relegation zone.
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Macclesfield Town manager Gary Simpson told BBC Radio Manchester:
"These are a good team, they've got some good players and I was wondering whether we had caught them at the right time.
"I'm highly delighted to get the points and first half we played some really good stuff.
"The lads were really happy they beat Bradford City and it shows you in what esteem they hold them because they're a massive club."
Bradford manager Phil Parkinson told BBC Radio Leeds:
"The lads have put in a tremendous performance, especially in the second half. I thought they were fantastic.
"In no way in a million years was that a penalty - absolutely no way.
"We had about 600 fans here tonight. All our staff and players were disgusted with the referee's performance and we can't all be wrong."