Facing a possible hefty fine and even a points deduction over four FA charges relating to the miss use of a football stadium grant Macclesfield needed to show a character to bounce back from a nightmare week.
Instead their defence frailties let the crowed booing as the team trudged off the pitch.
Macclesfield dominated the first half and went close when John Miles forced a fine save from Lee Harper with a 12 yard drive on the turn in the 24th minute.
Paul Harsley then went close with a curling 22 -yard chip that sailed inches past the upright.
However they gifted Northampton the lead in the 44th minute when Danny Swailes tripped Scott McGleish in the box the striker got up off the ground to thump home the penalty.
Macclesfield were again un done by a lack of concentration when Scott McGleish picked out former premiership star Ian Taylor who drilled a low shot into the corner from the edge of the box.
Macclesfield were given a life line when Martin Bullock lashed home his fifth goal of the season from 10 yards in the 61st minute.
They then nearly equalised only for Harper to brilliantly tip wide a snap shot from substitute Kevin Townson.
As the home side pressed forward, Northampton plugged the gaps in their leaky defence. In the 79th min David Hunt supplied sub Josh Lowe whose bullet drive was palmed into the path of McGleish to score from six yards.
Low added the final insult deep in injury time with a low drive from the angle inside the far post.