The turning point came in the 77th minute when former Premiership referee Andy D'Urso awarded a controversial penalty when Shaun Kelly got in the way of a Sean Hessey cross.
It allowed Gareth Evans to smash home a powerful spot kick giving Macclesfield a goal advantage, which they increased with a late strike from Martin Gritton as he bagged his sixth goal in eight games after 85 minutes.
The home side started the game more positively taking the lead in only the sixth minute when James Jennings picked out Nat Brown at the far post who bagged his fifth goal since coming on loan from Wrexham with a powerful downward header.
Evans went close to adding another on 20 minutes but his 25-yard shot from a narrow angle fizzed over the crossbar.
Chester only came to life on the half-hour when Kevin Ellison forced a full length save from Jon Brain with a skidding low drive.
Macclesfield looked to extend their lead before the break as both veteran striker Simon Yeo and Jennings tested the keeper with 15-yard shots. However, it was Chester who responded after the break, deservedly equalising on 56 minutes when livewire striker Ryan Lowe curled a delicate half-volley round the stranded Brain.
After Macclesfield's controversial penalty Lowe went close with a 20-yard snap-shot that was tipped over the bar but Macclesfield had the lion's share of late chances with Gritton heading over the crossbar and forcing a fine reaction stop from Danby with a powerful 10-yard volley.