Two goals in the second half by substitute Tshepo Chaine and Siyanda Ngubo in the 68th and 85th minute was enough give Amajita the victory.
South Africa could have opened the scoring as early as the 4th minute when Denwin Farmer’s glancing header went narrowly wide of the Ethiopian goal after the visitors were awarded a free-kick.
Two minutes later the hosts also saw their attempt go over the bar.
Ethiopia had more ball possession but could not penetrate the solid South African defence.
Ngubo came close again in the 28th minute, but his shot was stopped off the line with the keeper in no man’s land as the match went into the break goalless.
The home side nearly took the lead shortly after the restart with only goalkeeper Dumisani Msibi to beat, but he was equal to the task, using his legs to stop the shot.
In the 63rd minute Chaine ame on for Pule Maraisane and five minutes later the move paid off as Chaine scored into an empty net after Ngubo did all the hard work near the corner beating a defender before squaring passing to Chaine who made no mistake.
Five minutes before the final whistle South Africa got a free-kick and Maphosa Modiba floated it into the box where Ngubo pushed it past the goalkeeper to give the visitors a 2-0 lead ahead of the home second leg in two week’s time.
There was further drama when Gach Matay was red carded for a dangerous tackle on Chaine after the referee had blown the final whistle.