Usuthu sit only two points above the relegation zone after that result, which puts them in a precarious position heading into the final five games of the league season.
"This loss takes us to a very difficult situation as a club but I must emphasise that we were not comfortable because we were never in position one, personally I've never been comfortable," Johnson said.
"It's not good to lose at home because even your supporters go against you, it makes it very difficult and it's a very huge mountain to climb.
"For us to get out of this, it will need us to work on a very good technical plan and players to raise their hands and perform."
AmaZulu suffered two blows as their captain Nhlanhla Vilakazi and defender Tshapelo Nyongo were forced off due to injuries.
"It was not good to lose two important players, especially when we were trailing. I don't have an update on both but I'm more worried about Nyongo who got a kick around his knee, it looked very serious," he added.