Kinnear, who is already facing a Football Association charge of improper conduct for branding official Martin Atkinson "a Mickey Mouse referee", was sent from the bench by Mike Riley for comments made to one of his assistants in the wake of Abdoulaye Faye's injury-time equaliser in the 2-2 draw at St James' Park.
The former Wimbledon boss once again left coach Chris Hughton to conduct the post-match press conference, and he revealed the 61-year-old had been asked to leave the technical area after disputing the free-kick awarded against Sebastien Bassong for a foul on Ricardo Fuller in the run-up to the goal.
Hughton said: "I think it was for perceived comments, but from where I was, I certainly didn't hear anything. That's what I think it was for.
"Joe's okay, he is fine. He just felt that every now and again it is not a bad idea to have a little change of voice.
"One thing I can tell you is that it's a very, very emotional game, certainly at that stage of the game.
"The linesman had given a decision some four minutes before that, which having seen it again, is exactly the same as our thoughts were at the time - that it wasn't a free-kick.
"It was an old-fashioned shoulder charge, both players competing for the ball, and the free-kick was given.
"Some four minutes later, he give another free-kick in a similar position which again we felt wasn't a free-kick.
"To be fair to the lad Fuller he never tried to make a meal of it, he was on his feet, he had control of the ball.
"As I say, it is an emotional game particularly against a team who thrive on set-plays and free-kicks."
For the second successive home game, Newcastle squandered two points they could not afford to drop when they allowed a former player to snatch a point at the death.
Where Titus Bramble had done the trick for Wigan in a 2-2 draw at St James' Park on November 15, this time Faye turned up deep inside the penalty area in injury time to beat Shay Given and complete the fightback.
Stoke looked dead and buried when Michael Owen helped himself to a first-half double to give his side the perfect start.
The England international answered his critics in style with trademark ninth and 24th-minute finishes, and the Magpies looked to be cruising.
However, Danny Guthrie's failure to re-appear after the break forced a reshuffle from which his side never recovered, and City took full advantage.
Mamady Sidibe levelled on the hour as Newcastle turned in a dreadful display, and Faye, who had minutes earlier passed up a glorious opportunity, made no mistake at the second time of asking when substitute Glenn Whelan's free-kick eventually arrived at his feet.
Hughton said: "We would certainly look at it as two points lost, one, because we were winning the game reasonably comfortably at half-time, and the fact that it is a home game."