Ghana Captain Andrew Ayew scored the decisive goal from the penalty spot as the Black Stars advanced to the World Cup qualifying playoffs as winners of Group G on Sunday.
The Black Stars finish as group winners thanks to a tie-breaker of a superior number of goals scored with both teams finishing on 13 points.
Speaking after the final whistle, a disgruntled Broos hit out at referee Ndiaye Maguette and his handling of Sunday's tense encounter.
"I congratulate Ghana but I congratulate my boys also because we played against a very aggressive opponent which the referee allowed," Broos said.
"I am very disappointed in the result but I'm proud of my players. But I have to say, the referee today allowed Ghana to be too aggressive.
"I have nothing against aggressive play but it has to be legal aggression."
The Belgian though stopped short of criticising the referee's decision to award the Black Stars a controversial penalty.
"I couldn't see it. I just saw Daniel Amartey go down. He went down many times during the game, but I didn't see the incident. But I saw my players were surprised."
Former players and coaches including renowned names such as Steven Pienaar and Pitso Mosimane both broke their silence on the penalty call.
Pienaar, a former Bafana captain labelled the decision a "disgrace". While Mosimane called for VAR to be introduced on the African continent.