Manucho scored on his Africa Cup of Nations debut for Angola before Elrio van Heerden's superb late strike salvaged a point for South Africa.
Manucho celebrates his spectacular first-half goal
Manchester United bound-Manucho netted with a magnificent diving header in the first half after an incisive move.
With time running out Angola keeper Lama's wild punch resulted in the ball crossing the line, only for the goal to be ruled out for offside.
And Van Heerden's deadly strike ensured Angola had no second reprieve.
The draw was a fair result, and leaves all four teams in Group D with a point each.
The game produced plenty of entertainment, and the first half was very open.
South Africa's Teko Modise had the first chance, the midfielder cracking a shot from 30 yards that was punched away by Lama.
Four minutes later, at the other end, Flavio tried the same but his effort sailed over the bar.
Flavio had another chance midway through the half, slipping through the South Africa defence, but shooting into the hands of Moneeb Josephs.
But, using an attractive passing game, Bafana Bafana were having the better of the exchanges, and Angola's goal on 30 minutes came against the run of play.
Due to move to Manchester United, subject to a work permit, Manucho had been billed as one of the potential stars of the tournament.
And he could hardly have justified the hype more spectacularly, propelling in a Flavio cross with a diving header that was simply exceptional, following a flowing move.
The second period took a while to get going, with South Africa showing the greater urgency.
Angola nearly grabbed a second goal on 62 minutes, but substitute Ze Kalanga's long-range shot veered just wide.
On 71 minutes Flavio forced Josephs to make a save with his feet, but South Africa were to dominate the closing minutes.
Van Heerden's goal came from 20 yards out, another fine goal in a tournament that has provided plenty of exciting football thus far.
There was a lively atmosphere at the Tamale Sports Stadium, with vocal contingents of Angolans and South Africans.
South Africa: Josephs, Masilela, Morris, Moon, Mokoena, Tshabalala (Chabangu 46), Pienaar (Van Heerden 71), Modise, Mhlongo, Moriri (Fanteni 46), Zuma.
Subs Not Used: Fernandez, Khune, Evans, Fransman, Nhlapo, Dikgacoi, Davids, Mphela, Walaza.
Booked: Mokoena, Moon.
Goals: Van Heerden 87.
Angola: Lama, Airosa (Loco 89), Yamba Asha, Kali, Marques, Figueiredo (Ze Kalanga 64), Macanga, Gilberto, Mendonca (Edson 73), Flavio, Manucho.
Subs Not Used: Mario, Nuno, Delgado, Jamba, Machado, Dede, Mateus, Love, Maurito.
Goals: Manucho 29.
Ref: Koman Colubaly (Mali).