Referee Carl Sarginson's decision left Macclesfield manager Keith Alexander fuming, labelling his performance as scandalous.
With seconds ticking down at the end of first-half injury time, Scott Wiseman released Chris Dagnall who beat the cover before poking the ball past Jonny Brain and collapsing over his out-stretched body.
Brain was adamant he had committed no foul but the referee pointed to the spot and left-back Tom Kennedy duly converted.
Dale dominated the first half with powerful skipper Gary Jones sliding a shot inches wide in the 18th minute before Dagnall powered a header just over the bar two minutes later.
Then on 25 minutes, Brain made an outstanding save to deny Wiseman's drive from the edge of the box.
Macclesfield were out-played in the first half and only loan signing Emile Sinclair looked dangerous with a shot that was plucked out of the air by Frank Fielding in the 35th minute.
Macclesfield had their own appeals for a penalty turned down in the 61st minute when Jones appeared to upend Danny Thomas in the box only for the referee to give a free-kick on the edge of the 18-yard line.
Nat Brown powered a shot through a melee of players for Fielding to make a superb save grabbing the deflected ball.
Macclesfield again went close in the 75th minute when Tom Elliott bravely threaded the ball through to sub Gareth Evans only for Fielding to save the substitute's snapshot with a full-length dive.
At the death, Brown went close for Macclesfield with a header at the far post but could only direct it a foot wide of the angle.