Ubuntu took control of the tie in the first hour courtesy of goals from Clint Fredericks, Duncan Adonis and Kamohelo Mahlatse at King Zwelethini Stadium on Friday night.
Usuthu stirred and reduced the deficit via headers from Mabhuti Khenyeza and Ovidy Karuru, but they could make no further inroads as they twice hit the post in quick succession in the last 10 minutes.
Ubuntu also knocked Premiership outfit Polokwane City out of the competition in the previous round.
“I think if you watched the first half then you saw a comedy of errors. I think technically we were not... ja you make two mistakes in 15 minutes of the game and they are 2-0 up,” Johnson said.
“You ask yourself what are we doing? I think the biggest thing is you underestimate the team you are playing against in the first half and you underestimate in such a way that they are going to the changing room 2-0 up. Their tails are up and we’ve got to now come up and take the game to them.
“On top of that you have 80 percent possession and you can’t score the goals. You come back, you get one. You get two and you chase the third one and that doesn’t happen. But I don’t think we were... in the best form even in their last third.”
The tournament has delivered upsets in the past, such as when Maluti FET beat Orlando Pirates 4-1 in 2013 at the same stage of the competition.
“In all leagues all over the world you have these games and you lose them and you scratch your head for a moment after the game,” Johnson added.
“You try to pick the faults that happened and you try to pick the players that made the faults. You try and rectify it because that’s why we are coaches, to go back to the drawing board and try and fix it up.
“Yes, you’ll have these moments in your life as a coach. You got to pick yourself up as a coach and make it better for the next game.”
Johnson’s side, who are 13th on the Premiership log with 27 points from 23 matches, next face Kaizer Chiefs in the league on Saturday at FNB Stadium.