For the majority of the game the Owls were a far cry from the side which demolished Leeds 6-0 on Saturday, despite taking a third-minute lead through Chris Maguire.
After Scott Boden's penalty 65th-minute penalty brought the tie level, a giant-killing was in the offing when Scott Kay had the goal gaping shortly after.
But the Macclesfield midfielder hit the bar from just three yards and the Silkmen were made to pay for their missed opportunity.
Late efforts from Jacques Maghoma, Jermaine Johnson and Miguel Llera spared Wednesday blushes, meaning the home fans were able to enjoy another goal-fest as their side booked a fourth-round date at Rochdale.
Caretaker boss Stuart Gray had warned against it being a case of 'after the Lord Mayor's show' following Saturday's polished disposal of their Yorkshire rivals and it looked as if his Wednesday side took note as they needed just three minutes to take the lead.
Reda Johnson fed Maguire down the left and the striker ran with confidence, cut inside and sent a low shot past Rhys Taylor.
That was the catalyst for the dominant type of period of play you would expect from a side three divisions above their opponents and Wednesday could easily been three up by the midway point of the first half.
Maguire was the main threat throughout and sent a 20-yard effort whistling just wide before seeing a low effort cleared off the line by Joe Connor.
To their credit, the non-league outfit began to put up a fight and could have levelled but Jack Mackreth fired straight at Damian Martinez and Danny Whittaker flashed an effort past the post.
Wednesday, deprived of influential loanee Connor Wickham, went completely off the boil and looked devoid of attacking threat, perhaps giving an insight into to what life might be like after Wickham returns to Sunderland later this month.
And while Wednesday were only one goal to the good they were always susceptible to danger and so it proved midway through the second half as Macclesfield brought the tie level.
Substitute Chris Holroyd foraged into the area down the right and after Joe Mattock intervened with his hand, Boden coolly stroked the resulting penalty into the net.
The Silkmen were beginning to believe and the chance for them to take the lead was on a plate five minutes later but Kay was denied by Martinez and then inexplicably hit the rebound against the bar from close range.
But the Owls began to flex their muscles and soon regained their lead when Maghoma drilled a low finish across Taylor following Johnson's clever set-up.
Johnson gave his side breathing space with five minutes remaining with a 25-yard effort that skidded into the bottom corner and Llera's header from a corner at the death killed off a brave Macclesfield effort.