The Ivory Coast international looked to have cancelled out Edin Dzeko's opener when he drilled home from distance in the 34th minute, but after speaking to assistant Stephen Child, Jones ruled out the goal, much to the disgust of the Magpies faithful and manager Alan Pardew.
It appeared that Jones and his official ruled that Yoan Gouffran - who was stood in an offside position when Tiote struck the ball - was interfering with an opponent by distracting Manchester City goalkeeper Joe Hart.
"I don't understand why the referee didn't give the goal," Tiote told Sky Sports.
"I think it was Gouffran who was next to the goalie but he didn't touch it. I don't know why the assistant referee decided to give offside.
"That's football, we need to accept it and go forward.
"I'm so disappointed today but I think we played well and that's the most important thing. We can take it on to the next game."
The controversy raised the temperature at St James' Park for the remainder of the contest, with Newcastle pushing hard for an equaliser before Alvaro Negredo struck in added time to finally put the result to bed.
Pardew's angry touchline confrontation with City boss Manuel Pellegrini did nothing to calm the mood in the stands, with the Newcastle manager appearing to aim a foul-mouthed volley at the Chilean as they squared up.
"I apologise for that," Pardew told Sky Sports. "But he had words with me first and it was just normal for managers that go unseen most of the time.
"We're fine, I shook his hand at the end and I'll see him before I go."
Pardew tracked down referee Jones after the match to discuss the disallowed goal and revealed he was not satisfied with the answers he received.
"For me, this is an entertainment business. The guy's hit a goal that Joe Hart is just not going to save. It goes through a number of bodies but his vision is not impaired," he said.
"I don't think he was clear in his answers about Joe Hart being impaired - I couldn't work that out.
"I don't understand it. Even if Man City's back four is on the edge of the box and we've got four offside, it's such a clean hit, it's going in the top corner.
"He's got that wrong and unfortunately that was a massive call. In these type of games that have got to go your way.
"It was probably easier for him to give the goal and I can't understand why he hasn't.
"We're crying out for entertainment, you hit and goal like that the place is in uproar, and he's gone on a real tiny technicality, which I think is wrong."
Pellegrini unsurprisingly had a different take on the Tiote disallowed goal, saying only: "Of course it was absolutely offside."
The 60-year-old also had cause to feel aggrieved due to a second flashpoint in the match, which came in the 75th minute when Mapou Yanga-Mbiwa went in recklessly from the side on Samir Nasri.
The City midfielder required several minutes' of treatment before being taken off on a stretcher with his left leg in a brace, and Pellegrini felt Yanga-Mbiwa should have seen more than just a yellow card.
"The kick he made to Nasri was absolutely a red card directly," he told Sky Sports.
"We did not have any help from the referee today. He didn't give a goal because it was absolutely offside, that is the only clear thing about which Newcastle can complain - but it was offside."
Pellegrini fears Nasri suffered a "serious" medial ligament injury in the challenge with Yanga-Mbiwa.
"Nasri has I think a serious injury to his knee, we will see tomorrow. I repeat it was a direct red card," he said. "It's his medial ligament. We will see tomorrow what has happened with him."
Discussing his spat with Pardew, he added: "He was complaining all the decisions of the referee. Every time you whistle a foul he complained. I don't think that's the way to do it."
Asked if he had a problem with anything Pardew said to he, he said: "Nothing, nothing. No problem."