Eleazar Rodgers and Teko Modise netted second-half goals, with Modise clinical from the penalty spot, but only after Anthony Laffor had missed a first half penalty.
After the match, Neeskens said: "Overall over the 90 minutes we were the team that deserved to win.
"In the first half with the wind at our backs we tried to play forward and got some good shots off from distance.
"I'm not totally happy with our passing in final third, it was not good enough and of course we missed a penalty which was not good for our confidence.
"The second half they tried to come back but we controlled the match and got a second penalty that was deserved.
"Overall we must be happy but still we have a lot to improve. We will take it step by step. It is two games we didn't lose now so that's positive."
Looking ahead to his side's PSL clash with Orlando Pirates in midweek, Neeskens added: "It will be a tough game against Pirates but the players should be more confident after this result."
Usuthu boss Roger Palmgren was less than impressed with the result although he felt his side defended well all afternoon.
"I think we defended very well. We made a horrible mistake when they scored the first goal but we put up a good fight throughout the game.
"They were more clinical in front of goal but we have to keep up with our strong defence, keep on working like that, but also take care of the ball better in the offensive areas of the field."