The League Two visitors' early promise had threatened another round two shock but Wanderers' Premier League quality eventually told.
And it was Tuncay, the former Middlesbrough and Stoke forward, who was the catalyst for change.
The 29-year-old had been made to wait for almost two weeks for his work permit to come through in order to finalise his move from German side Wolfsburg.
Everything was eventually deemed to be in order on Monday and having been given his debut at the first available opportunity he made the most of the chance.
Played up front as a centre-forward, Tuncay looked much more comfortable in the second half when substitute Kevin Davies resumed his regular line-leading role and the Turk was moved to a role with more freedom on the right.
From there he could drift in and that was how he scored the first and made the second.
That is not to say he had not tried hard in the first half and he should have put his side ahead early on after Petrov had raced 60 yards down the left to cross but he blazed over under pressure from Carl Tremarco.
But the League Two side, trying to bridge a gap of 75 league places, were far from unsettled and took an 11th-minute lead when Tony Diagne's through-ball allowed Emile Sinclair to sprint clear of a flat-footed defence.
Adam Bogdan hesitated as he raced out of his area and the striker rounded the goalkeeper to slot into an empty net.
Robbie Blake, Darren Pratley, Chris Eagles and Zat Knight all went close in reply but Macclesfield were not prepared to sit back and defend and a quick break saw Sam Wedgbury's long-range drive fly over with Bogdan at full stretch.
Right on the half-hour Mark Davies' incisive crossfield ball with the outside of his right foot picked out Petrov on the left of the penalty area but the winger smashed his shot against the post.
Tuncay then flashed a header from Eagle's right-wing corner across the face of goal before Joe Riley, a 19-year-old Bolton academy debutant, even got in on the act with an angled drive which Veiga claimed at the second attempt as the visitors held on until the interval.
Kevin Davies' arrival for the second half certainly added more threat to the forward line and he almost scored with his first touch as when bundled Riley's low cross wide from close range.
Wanderers manager Owen Coyle was then forced to give an earlier-than-planned debut to another 19-year-old when Adam Blakeman replaced injured left-back Marcos Alonso.
But the pressure was building and after both Tuncay and Blake had forced Jose Veiga into saves at his near post Bolton scored a deserved 56th-minute equaliser.
Riley's right-wing cross dropped invitingly for Tuncay whose scissor-kick volley gave the Macclesfield goalkeeper no chance.
But if Bolton thought they had broken the visitors' resistance they were wrong as Diagne's low free-kick had Bogdan diving to his right to keep the ball from creeping inside the post.
But as the spectre of extra time loomed ever closer Bolton finally got their noses in front with Tuncay playing a pivotal role again.
His cleverly-lofted ball over the top of the defence was picked up by Petrov who fired home inside the near post.
Bolton's greater experience saw them home as they defended solidly and countered-attacked positively as Macclesfield's challenge ran out of steam and they missed out on the third round for the 15th successive season.