Jones received a straight red card in Saturday's 2-2 draw between the teams at the Stadium of Light for reacting angrily to a challenge from Herita Ilunga.
The big striker shoved the West Ham full-back to the ground, leaving referee Andre Marriner no option but to hand him his marching orders.
Afterwards Bruce was disappointed with Ilunga's reaction, questioning 'why does he need to roll around like that?' but Clarke strongly defended his player, believing the Black Cats boss should have kept his opinions to himself.
Clarke also questioned the antics of Sunderland captain Lorik Cana on the pitch.
He told Sky Sports News: "First of all, I think it was wrong of Steve Bruce to comment on our players - we have a manager who doesn't speak about any other teams' players, so I think that was wrong.
Incredible"He said what he said - I find it incredible that the player who was the victim is the person that everybody is talking about.
"You have to correct me - tell me what Ilunga did wrong? Someone pushed him in the face, he's just recently recovered from a triple fracture to the jaw, maybe he thought there was a punch coming.
"I find it incredible that we're sitting here speaking about our player who was the victim, this is wrong. It's completely wrong."
He insisted there was no over-reaction from Ilunga, adding the player had to protect himself.
"He's a big boy Kenwyne Jones, he's a very big boy. He had to look after himself," said Clarke.
"I find it incredible that he (Bruce) gets so much time, so much airtime if he wants to speak about people from the opposition.
Terrible tackle"I also find it incredible that the Sunderland captain wasn't sent-off - he was booked for a terrible tackle on Mark Noble, he kicked him up in the back.
"He was warned for a ridiculous lunge into the back of Mark Noble three or four minutes later.
"He then committed a two-footed tackle on Guillermo Franco in the centre circle which the referee knew he couldn't give as a free-kick as he would have had to send him off.
"And then after that he persistently fouled, another two-footed lunge in the second-half.
"You know it is easy to speak about other teams and other teams' players.
"I don't agree with it but if people are going to have a go at our players then I'm going to have a go back, I'm sorry."