The recently-acquired Zenit St Petersburg forward decided the game with a thumping 74th minute strike but it did little to paper over the cracks of a lacklustre Selecao display
It was a tumultuous return to his native country for Mano Menezes as his side's performance left the home fans disgruntled and frustrated for large parts. However, when Hulk drilled in an effort after 74 minutes there was a collective sigh of relief to ease the pressure on the coach somewhat.
In a match that Brazil were largely expected to dominate, it came as a surprise when South Africa forged the first opportunity of the game in the 12th minute. Siboniso Gaxa pushed forward down the right and got in behind Marcelo after a one-two with Dino Ndlovu. He attacked the goal unopposed but his shot lacked conviction and Diego Alves saved.
The Selecao responded well and five minutes later they tested the opposing keeper from a set piece. Neymar's delivery from deep was met by a powerful header from Dede but he put it straight down the middle and Itumeleng Khune turned the ball behind.
The Bafana Bafana were giving a good account of themselves with a physical display dampening the atmosphere on Brazil's Independence day. After wayward efforts from Oscar and Neymar, it was not until the 34th minute that Khune was forced to work again as he kept out Lucas Moura's powerful strike, albeit unorthodoxly.
But there was nothing unconventional about the keeper's next stop. Neymar sprung the offside trap and latched onto Dani Alves' through ball but he failed to put his shot either side of Khune who stayed big to deny the Santos youngster.
Greeted by boos and calls for Menezes' head at half time and things did not get much better after the restart. Lerato Chabangu lashed an effort narrowly over the bar and was only denied a tap-in by a goal-line clearance from Dede moments later after some terrific work by substitute Bernard Parker.
There were signs of life from Brazil as Leandro Damiao and Neymar fired efforts at goal but they were warned against over-comitting as Parker's drilled effort scraped the bar on the hour mark.
Menezes made a number of changes in an attempt to alter the momentum of the game which was increasingly swaying towards the confident South Africans.
One of those substitutions saw the introduction of Hulk and from a free kick he won, Neymar saw a spectacular free kick clawed away from the top corner by the impressive Khune.
However, the keeper was finally beaten five minutes later, much to the relief of the home crowd. Despite making a brilliant stop from David Luiz's initial effort from an acute angle, the rebound fell to Hulk and the Zenit St Petersburg forward rifled a volley into the back of the net.
Neymar came close to adding another moments later but with his header from Hulk's cross shaping up to go wide, the keeper gave it an extra touch just to make sure.
Nevertheless the Selecao saw out the game but their fans will be upset with such a poor showing on their retun home which they voiced with more boos at the final whistle. Gordon Igesund, however, can take pride in the performance of his South Africa side in his first game in charge.