Goals by Teboho Mokoena, Mothobi Mvala and a stoppage-time strike by Evidence Makgopa sealed a crucial away win for South Africa in their objective to qualify for the 2022 Qatar World Cup.
The win was not without controversy as the Belgian dramatically replaced Mabasa with Victor Letsoalo in the 35th minute with the scores goalless at that stage.
Broos admitted after the final whistle that it was a tough decision to take but one that was necessary.
"I know it's a little bit disappointing for Tshegofatso," Broos said post-match. "But he had difficulties.
"It was better for us that we made a change and I explained the reasons to him.
"We rehearsed this in training this week but I don't think he really understood what we asked of him.
"Therefore we had to substitute him after half an hour.
Broos also detailed the impact that a late enforced change to his starting line-up had after an injury to Vincent Pule.
"It's always a bad thing when just before kick-oof you have to change a player due to injury," Broos added.
"It's a loss for the team because everybody is focused on the start of the game and then suddenly ten minutes before the start a player gets injured.
"So I was a little bit afraid but I think that Kutumela did very well and he was also a guy alongside his 10 teammates who fought until the last minute."
The win sees Broos' side maintain their lead at the top of Group G with a return leg against Ethiopia to follow at the FNB Stadium on Tuesday.
Bafana lead Group G with 7 points after three matches played, one point ahead of Ghana (6) who defeated Zimbabwe by 3-1 to move into second place.
Kick-off for the return leg at FNB Stadium is at 18:00.