Mothiba was a 61st minute substitute for Peter Shalulile and within seconds he set up Marcelo Allende for what proved to be the only goal of the game at the Seshego Stadium.
The substitute then stepped up after Khulumani Ndamane was bundled over in the penalty area, but he wasn't able to bury his 74th minute spot kick.
He attempted an audacious Panenka penalty that was easily saved by Lindokuhle Mathebula in the Polokwane goal.
Sundowns though held on for all three points to move top of the league standings, two points clear of Orlando Pirates in second, with four matches remaining.
Speaking after the game, Cardoso said on Soccer Laduma: "Look, I was looking in the back for the balance and a little bit also in the sky. I confess, I didn't really understand what happened.
"I think the goalkeeper was on the other side, so he tried to play on that side.
"Look, Lebo is a very good penalty shooter, very good. If he didn't make the goal today, it was not because he didn't want to, just because he couldn't. So it's what it is, it's what it is."
Sundowns play Polokwane City again next and finish out their season against Kaizer Chiefs, Siwelele and TS Galaxy.
