In a round that was befitting of the world's top ranked player, McIlroy recorded 11 birdies and not a single bogey at Quail Hollow in a round that catapulted him to 18-under.
Overnight co-leader Webb Simpson is next best on 14-under, with Robert Streb, who held a share of the lead on Thursday and Friday, a further three shots back.
McIlroy bettered his own course record of 62 – a round he registered on the way to winning his maiden PGA Tour title in 2010 – with some superb shot making and a solid day on the greens.
The Ulsterman began with birdies on the third and the fifth before his round sparked into life after a par on the sixth. Birdies at the seventh, eighth and ninth saw McIlroy take the turn in 31, and he went on to birdie six of the opening seven holes on the back nine to put a round of 59 in sight.
However, there would be no sub-60 round on offer, with a pair of pars on the penultimate two holes – including a scrambled four on the 18th – seeing McIlroy fall short.
As far as highlights go there were many from McIlroy's round, with a his tee shot on the 14th a particular treat, with the 26-year-old driving the green on the 345-yard, par-four 14th.
Simpson endured a slightly quieter day, and will be frustrated to have finished with a bogey at the 18th. Birdies at the fifth and seventh saw the American shoot 34 on the front nine, with a birdie at the 13th and an eagle at the 15th ensuring that he remained in touch with McIlroy. However, the former US Open winner would blot his copybook at the final hole to sit four shots back.
Streb began the day poorly with a bogey at the first, and never really got his round going, with three of his five birdies followed by a bogey at the very next hole.
Phil Mickelson looked set to finish the day on 10-under too, but 'Lefty' slumped to a triple-bogey seventh on the 18th to end his charge. Four birdies on the front nine saw Mickelson take the turn in 32, but having double bogeyed the 18th on Thursday, the American went horribly wrong once more on the last as his tee shot found the water from where he was never able to recover.