Two first-half goals for Owen Coyle's side were the undoing of the League Two outfit, who battled valiantly to try and get back into the game, but were ultimately out-classed
The hosts got off to a brilliant start as Kevin Davies poked past the visitors' goalkeeper less than a minute into the match and they continued to press throughout the first period, eventually finding a second.
Bulgarian winger, Martin Petrov, doubled the hosts' advantage before the break, giving the League Two side quite a hill to climb, and although they gave it their best shot in the second-half, they fell some way short.
The result also means that Macclesfield have won just one of their last 22 FA Cup games against sides from higher divisions, drawing five and losing 16 in the process.
The match could barely have started any worse for the Silkmen, as they conceded inside 34 seconds after a dreadful error from young right-back John Bateson.
Bateson, who appeared to have enough time to clear, slipped after a miss-kick which, in turn, allowed Ivan Klasnic to cross for Kevin Davies to prod home from close range.
It left the minnows with a mountain to climb but, they rallied, forcing Bolton into a series of misplaced passes in their own half.
Tonight was Bolton's first match without Gary Cahill, with the centre-back completing his move to Chelsea on Monday and Bolton appeared to miss his authority at the back in a disjointed display.
With Macclesfield failing to capitalise on any spells of possession, the warning signs were there, and Bolton broke in numbers at every given opportunity and it was no surprise when Owen Coyle's men made it two.
Tuncay, who had failed to slip in Martin Petrov just minutes earlier, this time provided a lovely pass for the Bulgarian winger to run onto before he surprised Jose Veiga with an early strike which curled beyond the Cape Verde international at his near post.
Bolton were hungry for more and sensed their chance as Sam Ricketts and Klasnic both went close after good moves.
The Silkmen refused to give up without a fight though, and looked to grab a goal back before the break.
The closest they came throughout the entire first-half was when the talented Matty Hamshaw dummied the ball past Mark Davies before curling a shot just inches past Adam Bogdan's far post.
Despite opening up a two-goal lead and appearing in control of the match, the second half belonged to the visitors.
Bogdan was arguably the busier of the two keepers as he bailed his side out on several occasions, with the Hungarian making a key save to paw aside a Carl Tremarco effort at his near post.
Bolton's two subsitutes David N'Gog and Paul Robinson combined for the latter to drag just wide, but Macclesfield continued to threaten at the other end.
The underdogs should have netted when Waide Fairhurst somehow failed to convert Tremarco's inviting cross, while Elliott Hewitt and Colin Daniel might have done better from Hamshaw and Bateson centres respectively.
For all their hard work and Bolton's complacency though, the Silkmen must now focus on League matters as they were unable to make a telling contribution on the hosts' goal.
The home side will look to stave off relegation worries in the Premier League and can now look forward to a home tie against Swansea City in the fourth round.
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