Adam Stansfield opened the scoring for the Grecians before Richard Logan put his side further ahead in a one-sided first half.
Exeter created plenty of chances and could easily have won more comfortably.
Macclesfield had the first chance of the game when Emile Sinclair darted into the box and flashed a shot past the post in the fifth minute.
But it was the Grecians who took the lead when Dean Moxey picked out Stansfield with a fine cross and the striker volleyed the ball home at the near post from close range.
The Grecians had plenty of chances to increase the scoring. Marcus Stewart could have made it two when he was found by Stansfield but the striker steered the ball wide.
Stansfield then had a header cleared off the line as Exeter continued to look the better side.
Just before half-time Manny Panther went close with a close-range shot after he was picked out by Stansfield.
A minute before the break Stewart picked out Logan and his shot from 20 yards took a deflection and flew past the helpless Jon Brain.
Ten minutes after the restart Matt Gill came close to hitting a third for Exeter when his long-range strike was tipped over at full stretch by Brain.
Substitute Craig McAllister found Stewart and the striker fired wide as Exeter continued to dominate.
The Grecians then struck two goals in as many minutes. Gill struck the ball against the post and Saunders tapped home the rebound.
McAllister then had a shot parried by Brain and the substitute was first to react and converted the rebound.