Naidoo, who had a share of the second-round lead after it was completed earlier on Saturday, narrowly missed a birdie putt on the 18th as the last three-ball finished in the dark when poor weather saw the field race to complete the round.
The 27-year-old Naidoo, 466th in golf’s world rankings, played a steady round with two birdies and a single bogey for a one-under-par 71, which gave him a three-round total of 202.
Canter, who won on the DP World Tour in Bahrain at the start of last month, had a much more eventful round after recovering from a double bogey on the first hole to shoot a four-under-par 68. His round included an eagle and six birdies but two more bogeys.
Marco Penge from England climbed into third place with his 68 taking him to 13 under par while the South African trio of Darren Fichardt, Branden Grace and amateur Christian Maas were 12 under.
The 21-year-old Maas was the only amateur to avoid the cut and shot an impressive 70.
Joint second-round leader Shaun Norris fell back to 10 under, shooting 76 after his putter let him down.