Making up for time lost to three lengthy rain delays on the opening two days, the entire field returned to the Serapong Course at the crack of dawn, and the Italian climbed to the top of the leaderboard on 11-under for the $6 million tournament.
The 19-year-old, seeking a third European Tour victory, resumed his round on the fourth hole and immediately reeled off four successive birdies, before adding two more on his back nine to sign for a bogey-free seven-under 64.
The players then headed straight back to the course to start their final rounds, hoping the thunderstorms that almost reduced the event to 54 holes stay away long enough to complete the tournament on Sunday.
South Africa's Louis Oosthuizen sits alone in second place on nine-under par after the 2010 British Open winner fired a six-under 65 to move a stroke clear of Briton Chris Wood.
Three-times Singapore Open champion Adam Scott of Australia remains on course to mount a challenge for a fourth title after a two-under 69 left him four strokes adrift of Manassero.
Overnight leader Thomas Bjorn, on the other hand, had a round to forget.
The Dane started the day one clear of Wood after going 27 holes without dropping a shot, but he bogeyed his second hole on resumption and struggled to a four-over 39 for his back-nine to slip five shots off the lead.
World number one Rory McIlroy was unable to improve on his overnight score of four-under after nine holes of his third round, as the Briton returned to play par golf for the remaining nine to sit seven back of Manassero and out of contention.
"Yeah, that kind of summed up the week for me really," said McIlroy.
"I've given myself plenty of chances on the greens, but just haven't been able to take them. I'm struggling to read the greens because I feel like I'm hitting good putts, but just not on the right lines."
McIlroy can claim the European Tour Order of Merit award with a top-three finish here and while it would take a huge turnaround for the Northern Irishman, he has not given up entirely on claiming an unlikely victory.
"It depends what the leaders do on the back nine," he added. "It's a tough course but there are plenty of birdie chances out there, so if I can shoot one in the low 60s and get into double digits under par, you never know what can happen."