Dejan Kulusevski earned injury-hit Spurs a deserved point with a last-minute header but City were left furious deep in stoppage time when Jack Grealish was through on goal only for referee Simon Hooper to stop play for a foul on Erling Haaland during the build-up.
Grealish appeared set to run through and score his second goal of the game to earn a dramatic win, but instead dropped two points to drop to third place in the Premier League and three points behind Arsenal.
Asked after the game for his thoughts on the incident, Guardiola told Sky Sports: "Next question. I will not do a Mikel Arteta comment.
"It is hard when you review the image, the referee decides to blow the whistle after he has already said to play on. After the pass, the whistle, so I do not understand this action.
"It was a good game, that is the most important thing. It was a pity, same as the Liverpool game, I had the feeling that today that we made an incredible performance in all departments, against a really good team and manager and how they play.
"We created a lot of chances, we were aggressive, incredibly concentrated, and the feeling is that we still want to be there [at the top of the table]. It is a pity. Sometimes football is like life, you do not get what you deserve."
Guardiola added to BBC Sport: "Sometimes I lose my mind about the referees, but here no. Always people can make mistakes.
"It surprised me for the fact that he went to whistle when Erling went down, after he stood back up and made the pass so the refereee made the gesture to play on. But then when the ball goes to Jack, then the whistle. That makes you think *gasps argh*.
"If in the right moment when Erling went down he whistled then you say 'ok', but whistling after saying play on... I don't know. It was a good game, everyone enjoyed it. Spurs are so happy, we are less so. Next on to Villa Park for the next game and to go again."
Arteta is currently in hot water for his comments around officiating after lashing out at the standard of referees following Arsenal’s 1-0 defeat to Newcastle last month.
The Gunners boss labelled the decision to award Anthony Gordon’s winning goal “embarrassing” and a “disgrace”, which has led to him being charged by the FA.
Arteta is waiting to learn what punishment he may get.