The pair are in a group tied for 15th place on five under par, seven shots behind leader and home favourite Charl Schwartzel.
MacIntyre, pictured, playing in only the third event of his rookie season on the European Tour, had eagles at the sixth and tenth holes on the Firethorn course, as well as four birdies on his way to a four-under par round of 67 which would have been even better but for a double bogey on the 17th.
Ferguson, the former British Boys champion, shot a 68 on the same course, a round which included seven birdies and an eagle before he came a cropper at the end, dropping two strokes at the 17th and one on the 18th.
Schwartzel will take a one-shot lead into the weekend after firing an excellent bogey-free 63.
The 2011 Masters champion is looking for a first win since 2016 and made six birdies and a spectacular eagle over the Bushwillow course to get to 12 under.
Zambian Madalitso Muthiya was at 11 under, a shot clear of 2010 Open champion Louis Oosthuizen, fellow South African Zander Lombard and America’s Kurt Kitayama.
Birdies at the first and fifth helped Schwartzel turn in 33 and he was edging into contention after further gains on the 11th, 12th and 14th.
A long putt on the 16th had him within one of the lead and despite having to lay up on the 17th after a poor tee-shot, he spun his third into the cup on the par five for an eagle.
The South African has six top fives without a victory at his home open.
Muthiya carded a 68 on the Firethorn course.