Jose Cordoba broke the deadlock with the game's opening goal after 58 minutes. Mbekezeli Mbokazi levelled with a long-range strike six minutes later, but Jiovany Ramos secured the win for Panama with his goal in the 77th minute.
It was the first time the Central American nation had been an African side and follows on from Friday's 1-1 friendly draw in Durban.
Both sides are using the game as preparation for their upcoming FIFA 2026 World Cup campaigns, where Bafana have been drawn in Group A alongside co-hosts Mexico, South Korea and the Czech Republic.
Speaking after the game, Broos revealed that his side had opportunities to score but were undone by a physical second-half showing from their visitors. Nevertheless, he expressed his happiness with both games against Panama.
“In the first half we had three open chances and didn't score,” the coach told SABC.
"In the second half we were overpowered by Panama. They had more power and speed than us and we couldn't play our game.
"This was a good test for us, we now know what international football is from other continents. I am very happy we played Panama. What we didn't do on Friday – win the game – is what Panama did today."
"These were very interesting games for us, and it will not make my choice (for my World Cup squad) any easier. I saw things I didn't know before these games," Broos added.