Trevor Benjamin started the rot with two goals at the beginning of the second half to stretch his side's unbeaten run to four games.
Benjamin equalled his tally for the whole of last season with two strikes in as many minutes and was only denied a hat-trick by a fine save from Jonathan Brain, with Macclesfield down to ten men after midfielder Kevin McIntyre was shown a straight red card for an over the top challenge.
Peterborough dominated the opening half and Macclesfield had to rely on the sharp reflexes of Brain to stay in the hunt.
The 23-year-old goalkeeper, making his first appearance of the season, went full stretch to deny Simon Yeo before clawing a Benjamin header from beneath the angle of post and crossbar.
Brain had luck with him just before the break when blocking a Yeo drive with his feet and the Town defence was glad of a helping hand from front man Matty McNeil, who dropped back to make two vital headed clearances as the Posh centres poured in.
Local lad McNeil also carved out Macclesfield's only real opening in the first 45 minutes, getting away from Chris Plummer to hit a low left-footed shot that advancing home 'keeper Mark Tyler saved well.
Macclesfield hardly knew what had hit them when Benjamin struck as the second half opened.
The Posh man's first, just 30 seconds after the break, was a diving header from Jamie Day's perfectly flighted cross and number two came when Benjamin pounced on a rebound after Brain saved brilliantly from Day's fierce close-range shot.
Brian Horton's men found themselves with an even bigger mountain to climb following McIntyre's dismissal and it needed another impressive stop from Brain, diving to his right to deny Benjamin his hat-trick.
But the goalkeeper had no luck in the 61st minute, saving a Yeo shot only to see the ball hit the shin of Andy Teague and flash into the net for Peterborough's third.
Amazingly, Macclesfield managed to have the last word with skipper Danny Swailes leading an injury-time break to squeeze the ball past Tyler.