Oswin Appollis (42'), Mohau Nkota (61') and Yaya Sithole (68') were all on target at the Nelson Mandela Bay Stadium, ahead of a late Joseph Banda strike.
South Africa are currently preparing for the upcoming Africa Cup of Nations, and take on Egypt, Angola and Zimbabwe when the tournament kicks off in December.
But despite this one-sided result, Broos explained that his side played below their level.
He said on SABC Sport after the game: "When I said we didn't do that enough today, we were a little bit soft.
"The tempo of the game was not high, in certain moments was not high enough. But ok that can happen and it happened today and it happened once."
Broos made a number of changes throughout the tie, including the introduction of Nkota for Appollis at the start of the second half.
Apart from his goal, the Orlando Pirates attacker also provided an assist.
“I think Mohau had a very good game, he was very aggressive, quick also dangerous,” added the head coach.
"Today we liked to do that (make changes) because it was the last time we can do that and that's why at half-time we changed a lot and it was not really good for the team and it's normal when you come in for new players it's a little bit annoying for everyone.
"But ok I think we didn't play our best game today but there were good moments and the moments we did what we had to do. The forwards was running, the forwards passes make us dangerous and it's also where we scored," said Broos.
