The Silkmen came from a goal down to lead 2-1 before David Wheater's header made it 2-2.
Macclesfield had trailed to Ivan Klasnic's close-range finish before Colin Daniel equalised, then Arnaud Mendy's stunning volley gave the home side the lead.
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 took the game to the visitors. And 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 Adam Bogdan.
In the 68th minute 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.