Macclesfield replaced striker Tipton with Eaton on 70 minutes and the youngster made an impact within a minute firing home their second goal.
Lightbourne put over a superb cross from the left and Eaton met the ball with a firm, diving header from within the six-yard box.
The game seemed over for Harriers who replaced debutant Coleman with Doyle on 76 minutes.
But the visitors almost made it three 10 minutes from time with Abbey's 25-yarder whizzing just past Brock's left-hand post.
The home side made their second substitution on 82 minutes, replacing Williams with Smith.
But they were still struggling to find the net or indeed seriously test keeper Wilson.
Macclesfield made their final change two minutes from time with Robinson on for Whitaker.
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