Broos has reinvigorated the senior national team since taking over by winning four, drawing one and losing just one of the six group matches.
This has meant Bafana will not be at the World Cup for the third time in a row after also missing out in Brazil 2014 and Russia 2018 having also missed out in 1994 and 2006.
"I'm disappointed today because we were very close," says Broos.
"We did very well in the last three months because nobody would have told you that we would be first before the last game. From that side, we did a very good job and there is a team in South Africa and that is very important.
"And again, I'm not happy with the way the referee let Ghana play in an aggressive way, I have nothing against that, but it must be for both sides and that was not the case today. It was difficult for us to have a good result here today but from the last three months, I'm proud of my team.
As previously mentioned, Broos emphasised that the plan remains intact with qualification for the 2023 AFCON finals the prime target for his side.
"We came here, and we tried to play a good game to maybe draw or even win. When you are so close and in the position that we were in you try to do it but again we played against a strong team with ten times more experience than us.
"We are a new team so you cannot blame South Africa for not having qualified for the next round. Not all. But you can be sure that there is a team in South Africa and that we will see in the next qualifiers for AFCON that we will try and qualify for the (2023) AFCON," Broos points out.
Bafana have only failed to qualify for five AFCON finals since the country was readmitted to international football.