Guardiola's side failed to win for the first time in 16 Premier League games dating back to last season as a result of the latest VAR row.
The champions thought they had stolen the points when Gabriel Jesus fired home in stoppage-time, only for the goal to be disallowed for handball after a replay review showed Aymeric Laporte had flicked the ball on with his arm.
It was the second time City have been frustrated by VAR against Tottenham following last season's Champions League quarter-final second leg when Fernando Llorente scored for Mauricio Pochettino's team despite a potential handball, while Raheem Sterling had what would have been the winner ruled out for offside.
"I thought we left that situation in Tottenham in the Champions League last season. But it is the same. The referee and VAR disallow it. It's the second time it's happened. It's honestly tough but it's the way it is," Guardiola said.
Deja vu for Man City as VAR saves Spurs again
"It happened last week with Wolves (against Leicester) and we saw for Chelsea on Wednesday -- the keeper wasn't on his line -- Adrian in the penalty shoot-out. They have to fix it.
"The whistle inside matches now isn't quite clear. But they believe it's hands with Llorente in the Champions League and sometimes they don't.
"It was incredible it wasn't a penalty in the first half (for the foul on Rodri in the box) but VAR said it wasn't and then at the end they did."
Tottenham manager Mauricio Pochettino shared a touchline conversation with Guardiola immediately after the goal was disallowed and after the match the Argentine joked he was "in love with VAR".
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"I didn't agree when we started to talk about VAR, but sometimes you get the benefit like today and in the Champions League (last season)," Pochettino said.
"Of course it is difficult to accept because we love the football from 30 years ago where it was more the decision of the referee - sometimes unfair things happen but at the end of the season we find a good balance.
"But we need to accept a different era and technology is in football now. We need to accept that today it is a benefit for us and when it is against us we have to deal with it with patience."
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