Sipho Mbule scored the only goal of the game at Dobsonville Stadium with a superb strike with 58 minutes on the clock.
South Africa get their AFCON charge underway against Angola on Monday and Broos is expecting an improved showing.
Speaking after the midweek game, the Belgian told SABC sport: "Let's say I am happy with the result, but we can play much better.
"We didn't play very well, we didn't have the movement we are used to with this team.
"Our passing was not good, so there is still a lot of work to do for us to be at the highest level this week.
"Maybe there was something in the players head that next week the AFCON starts and they are a bit afraid to be injured or whatever. Again, we expected more. But this can happen, I remember two years ago we were also terrible against Lesotho, so that gives us hope," added Broos.
"I am sure the boys will be ready next week against Angola"
Bafana are in Group B that also features Egypt and Zimbabwe.
Hugo Broos has named a 38-man preliminary squad for South Africa national football team ahead of international friendlies against Panama national football team later this month, giving several overlooked players another chance to impress.
Orlando Pirates veteran midfielder Makhehleni 'Cash' Makhaula believes the club's rising stars could form the backbone of Bafana Bafana's squad at the 2026 FIFA World Cup.
Ghana forward Antoine Semenyo has explained how he has been able to adjust to Manchester City following his January transfer window move from Bournemouth.
Bafana Bafana's kit for the upcoming World Cup has been unveiled by the South African Football Association.
