The 40-year-old Nomvethe - the PSL's record scorer with 120 goals - last featured off the bench against Cape Town City on December 15 at Cape Town Stadium for his eighth appearance of the season.
Some of the talk going round is that Nomvethe spoke with supporters at his home and incited them to rally against Johnson.
Usuthu consequently called a press conference in Durban on Wednesday where they put out a united front.
The club's general manager Lunga Sokhela said: "The reason why I requested this press conference is because it involves one of South Africa’s greatest players of recent times. A man whose record speaks for itself and a critical member of the AmaZulu family.
"We’ve called him in to comment for himself on certain issues but firstly before I get there, I’d like the media to understand that as a club we hold Mr Siyabonga Nomvethe at a very high calibre and as AmaZulu Football Club we are privileged to have him as part of us.
"His role at this stage of his career is not just limited to him being on the field of play but also in guiding other young players within the squad to replicate his heroics. He’s a role model on and off the field and as management we love him greatly.
"He’s very much part of the club and the club’s plans going forward. I’ve been at pains through the years at AmaZulu to engage properly when there’s areas of discontent.
"Recently it has come to my ears that supporters are discontent with the lack of game-time that Mr Siyabonga Nomvethe has been getting.
"Some media reporters further say that Mr Nomvethe is actively calling supporters to his home to incite them to boycott the coach.
"To me if the above is reportedly true than it is unacceptable and I’ve exercised enough patience in this matter."
Nomvethe insisted there was no substance to the rumours and reiterated his respect for Johnson.
"I was surprised to see things written and I’m not someone who reads newspapers. I’ve never done anything wrong, ever since I’ve started to play football," 'Bhele' said.
"I respect everything that is happening within the team and I respect the club’s flag, and I respect even the coach and the technical staff and management.
"At the age I am I’ll not do funny things because I know myself. I’m a person who is very reserved. I’m someone who likes to work hard on the field of play.
"I always report on time for training and I never fight with anyone, even the coach. Even what has been said, I never called supporters [to my house] but I have to protect the club’s flag and protect my family.
"I’ll never do funny things to invite people in my house because most of the time I spend time at home.
"I’ve never thought in my football career that there’ll be things said like this about me. But the way it happened, I was completely surprised to be shown stories written down that I’ve invited fans to have a bad influence to say, 'let them hit the coach’. I’ve never had a problem with the coach ever since he came to the club."
Johnson said: "For myself as the coach, I think there’s two sides to the story but the one side you read the other day is the wrong side; it’s either left side or right side.
"I don’t think as the AmaZulu family, and it has been said by Lunga and it has been said by Bhele Nomvethe, that we are building... and building big.
"There’s always people, that when you climb the mountain, there’s always someone at the bottom trying to pull you down and that happens in life.
"But if you build it properly then the structure within AmaZulu will be as strong as it is now. When you hear these gentlemen speak [Nomvethe and Sokhela] they speak positively about AmaZulu.
"Whoever wants to speak negatively about AmaZulu, from this day forward, I don’t think you’ll get anywhere. Whether you are in the media, whether you are on TV, or whether you are an ex-player, you’ve got to realise that the ground that we are building on will always be green and it’ll be strong... and it’s going to take lot to break it down.
"But we as a club, like Brilliant Mkhathini [media officer] has said, we have to nip this in the bud. Lastly, we don’t have any problem with the players in our club. I don’t believe Nomvethe, with the professional that he is, is capable of doing that."