Reeve Frosler thought he had earned the Clever Boys a penalty in the seventh minute after his fierce strike from outside the box hit Tebogo Langerman on the arm inside the penalty box, but the referee waved away their appeals.
Thapelo Morena had the first chance of the match in open play in the 17th minute after being sent through on goal by Sibusiso Vilakazi, but his shot from the edge of the box was brilliantly parried away by Darren Keet.
The intensity of the match after half-an-hour was terrific with chances created from both ends of the pitch.
Percy Tau had a wonderful opportunity to grab the lead for the Brazilians in the 32nd minute after beating the offside trap but Sifiso Hlanti made a timely tackle to deny the attacker.
Vilakazi could have opened the scoring five minutes before halftime but his wonderful strike from just outside the box hit the corner of the crossbar.
The first stanza ended scoreless despite many chances created.
Two minutes into the second half, Tebogo Langerman delivered a great cross from the left wing that Tau controlled beautifully inside the box with his left foot but his strike sailed over the bar.
Mosimane introduced Khama Billiat four minutes before the hour mark in place of Morena.
Hlompho Kekana nearly caught Keet off his line with a looping strike on the hour-mark from in his own half but the ball sailed a few metres behind the right post.
Billiat had an immediate contribution as he broke the deadlock in the 63rd minute by turning home Tau's inch-perfect cross from the left flank.
The Brazilians were under pressure after 70 minutes as the Clever Boys kept pushing for an equaliser, while Gavin Hunt also introduced James Keene.
Vilakazi should have sent the visitors into a two-goal lead in the 75th minute but his low shot from inside the penalty box was saved by Keet.
Billiat eventually made it 2-0 in the 81st minute after being sent through on the edge of the box and he hit a left-footed strike into the bottom left corner.
Anthony Laffor should have ended the game as a contest after going through on goal three minutes before time following a counter-attack but he opted to pass in the behind of Billiat instead of going for goal at close range and it finished 2-0 in favour of the Brazilians.