Stuart Baxter made one from the team that hammered Seychelles 6-0 in the first leg, with Dino Ndlovu taking Aubrey Modiba's place in the starting line-up.
As Group E table-toppers, all eyes were on the visiting team to see if they would replicate the same performance they dished out at the FNB Stadium last weekend.
But it wasn't to be as Seychelles bagged their first point of the Afcon campaign after 90 minutes.
Seychelles made it difficult for Bafana in the first half, giving them no space to move the ball around, especially in midfield where Dean Furman and Kamohelo Mokotjo were playing.
For the home side, this was always going to be a difficult match and it wasn't surprising to see them throwing numbers behind the ball in protection of their goalkeeper.
They relied heavily on counter-attacks, although they often struggled to get past the Bafana back four which was marshaled by Thulani Hlatshwayo and Buhle Mkhwanazi.
Having scored thrice in the opening 45 minutes of the first leg, Bafana were expected to start with the same energy, but they somehow found it difficult to even create some clear-cut chances.
Percy Tau, Lebohang Maboe, Lebo Mothiba as well as Dino Ndlovu were always surrounded by two or more players whenever they had the ball, and while Baxter's intentions were clear from the start with his very attacking line-up, his team's failure to test the Seychelles goalkeeper should be worrying.
Chances were few and far between with Ndlovu and Tau the only two players that came close to scoring from distance.
However, their shots at goal didn't trouble the Seychelles goalkeeper, who hardly had anything to do in the first half.
In fact, Bafana were lucky to survive a late first half scare as Seychelles invaded Itumeleng Khune's penalty before whipping the ball into the dangerous area, but the Kaizer Chiefs goalkeeper was alert to make a save.
For a team that has scored a single goal so far in this campaign, a goal against Bafana would have definitely done wonders to their confidence.
A dominant display that saw Bafana amass a whopping 77 percent ball possession after the 45 minutes was certainly never going to please or be enough in the eyes of the South African public, and Baxter needed a change of plan in the second half.
There was a change in attitude from Bafana players after the restart as they created two goalscoring chances inside the opening three minutes of the second half.
Ndlovu, who scored his first international goal last weekend, combined well with Mothiba inside the Seychelles box, but the France-based striker hit the woodwork from close range.
Mothiba tested the goalkeeper with a tame shot seconds later as he appeared indecisive after some good footwork by the team.
The pressure was starting to mount on the home side, who often found themselves having to deal with Bafana's attackers more than they were in the first half.
Tau thought he had broken the deadlock after 55 minutes, but despite finding the back of the net, the flag on the side had already gone up for offside.
Bafana came into the encounter with an average of 2.7 goals per match in this campaign, and very people expected them to struggle against the Islanders, who had conceded 14 goals in the three games.
Bafana's away record in the Afcon qualifiers was also expected to be a factor in deciding who walks away with all the points in the Seychelles - 12 victories 11 draws and nine losses - but they failed to increase their wins this time around.
Furman tested Dingwall with a fierce shot towards the end of the game, but the Seychelles goalkeeper did brilliantly to stop the shot and keep his team in the game.
In the end, both nations settled for a share of the spoils; the result which would feel like a defeat for the South Africans.