Sundowns ran out 1-0 winners against Kaitano Tembo's charges in the Nedbank Cup last 32, with Morena setting up Sibusiso Vilakazi for the game's only goal.
"I haven't got the full update on him. Very sad, we need Thapelo for Champions League and I think the ankle came off, I don't know but I think they managed to put it back. I'm not sure about that," Mosimane told SuperSport TV.
"The pitch is soft so I think it (Morena's ankle) got stuck in there and couldn't get the leg out. Disappointed with that because we need him for Champions League and we need him for the rest of the season. But football is a professional sport so these things do happen," he added.
According to Mosimane, his former side looked more 'dangerous' and a 'better playing team' with a possession-based model after playing in 'two formats'.
"A difficult game for us, I think SuperSport played in two formats. They looked more dangerous and a better playing team when they were passing the ball around and they made us to defend a lot.
"But they changed the strategy when it was 15 minutes to go and they played into our hands…they played the long balls and we have Mosa (Lebusa) who took out all the aerial balls.
"Ricardo (Nascimento) took all the aerial balls, (Motjeka) Madisha took them same as Anele (Ngcongca) they are good in aerial strength and that did not help them.
"I think they could've hurt us if they continued playing the way they were playing. But we played the level of Champions League. We can play quiet, loud. Tonight we played quiet and we are through to the final (second round)," Mosimane stated.