Sundowns raced into a 2-0 lead with goals inside seven minutes from Bangaly Soumahoro and Ricardo Nascimento (penalty), and then had a header from Leonardo Castro harshly ruled out for an infringement in the build-up.
They wasted further opportunities and were punished when Geoffrey Sserunkuma grabbed what could prove to be a vital away goal for the Ugandans in the second half.
“We played against a very good team, they are organised and they play football,” Mosimane told SuperSport TV. “We let ourselves down. We should have not allowed the goal. But we still won the game and we will go and fight in Uganda. We have put ourselves in this situation, so we should not complain.
“The boys were a little bit emotional, their passes were not the right options. It also showed a little bit the inexperience of Percy [Tau], he’s still young and still needs to get there.
“The goal we scored [by Castro] was a goal, I don’t think there was a foul there. But it’s OK, we have a team to go there [Uganda] and do well.”
The return fixture will be played in Kampala next Saturday.