City exited the competition after a goalless draw with Wits last night, having lost 3-0 in the previous meeting at Bidvest Stadium.
Manyama sees the experience as a learning curve as Eric Tinkler's newly formed side find their feet in the topflight.
Manyama told SuperSport: "We tried our best but in all honesty I mean this game was long gone from the first leg. We lost it in the first leg but we had to come here and show that we are the home team. We tried our best you know but we played the better team. For us it's still a learning curve all we have to do is congratulate them."
The former Ajax Cape Town winger added: "You know if we got one (goal) it would have been better for us and we kept on looking for it. These things don't come sometimes and you have to accept it. But at least we tried, we're creating chances, we just need to take
one and then we''ll take it from there."
City came into existence in the off-season after ex-Ajax boss John Comitis bought the top-tier status of Mpumalanga Black Aces.