David Wheater's late header rescued Bolton from the verge of becoming giantkilling victims after the Silkmen's tired legs finally gave in.
Before then, Arnaud Mendy's spectacular volley had given the League Two side real hope of an upset and a place in the fourth round.
Ivan Klasnic had given Owen Coyle's side an early lead, before Colin Daniel fired Macclesfield level, and the Silkmen had dominated much of the match until they ran out of steam. The tie was played against the background of the first anniversary of the death of Macclesfield's popular midfielder Richard Butcher, who died at the age of 29 from a rare heart condition.
Silkmen manager Gary Simpson, as he does for every match, wore the number 21 in memory of Butcher, as well as yellow socks in honour of Keith Alexander, who died in 2010 aged 53 when Simpson was his assistant at the Moss Rose stadium.
Macclesfield started brightly but the Premier League side took the lead in the seventh minute.
The Silkmen's keeper Jose Veiga had done well to turn aside Chris Eagles' strike but from the following corner Klasnic pounced from close range after the home side failed to clear.
Macclesfield could easily have folded after such a disheartening start but instead they took the game to the visitors.
Daniel could have had an immediate reply when he went through one-on-one with Adam Bogdan but the Bolton keeper came out well to deny him.
Bogdan then produced more heroics to keep out Mendy's sharp strike from 20 yards.
But the pressure finally told in the 15th minute when George Donnelly burst down the left, found Daniel unmarked at the far side of the area and he kept his cool before burying a fierce low shot past Bogdan.
Bolton full-back Joe Riley skimmed the top of the bar with a cross-cum-shot from deep on the right, before Wheater picked up a booking for felling Matthew Hamshaw in his tracks.
The home crowd howled for a red card but there was cover coming across and referee Jonathan Moss made the right decision in showing yellow.
Macclesfield continued to enjoy the bulk of possession and peppered Bolton with long throws and corners, and early in the second half Carl Tremarco's excellent cross from the left reached Daniel but his header lacked the power to trouble Bogdan.
Bolton were then grateful to Wheater for a last-ditch tackle to deny Sam Wedgbury as he ran onto Hamshaw's throughball, before Bogdan did well to save smartly from Daniel's low strike.
Riley prevented an almost certain goal with a tremendous block of Donnelly's shot from eight yards, and although Tremarco had another effort on goal from the ensuing corner it was straightforward for Bogdan.
In the 68th minute however, the game swung towards Macclesfield, and in stunning style.
Wheater's attempted headed clearance failed to make any distance and, from 25 yards out Mendy flicked the ball up before producing a beautiful volley into the top corner.
The 21-year-old French-born Guinea-Bissau midfielder turned away in restrained celebration while his team-mates and most of the 5,757 inside the stadium went crazy.
Dreams of a famous victory proved short-lived however as Wheater headed Bolton back level 13 minutes from time.
Martin Petrov's free-kick from the left was expertly delivered and Wheater held off his marker to head down and past a flat-footed Veiga.
Macclesfield's endeavours looked to have tired them out, and Eagles looked for a winner with a curling effort from the edge of the box but it was too high.
Petrov then struck the angle from a direct free-kick before Veiga's stunning block denied Klasnic in the last minute - and that was only fair on Macclesfield who at least deserved the benefits of a replay.
