Liverpool's Mohamed Salah, who now leads the race for the Golden Boot, expressed his disbelief over the decision on Twitter - as did a number of other footballers including Virgil van Dijk and Jamie Vardy.
Sadio Mane opened the scoring in the first half before the Egypt worldwide netted his 30th goal in the Premier League with a superb header over Asmir Begovic.
In that time Spurs have all-but booked their Champions League spot for a third successive season and they could pour more misery on a faltering City side. I think Harry is a very honest person, he's not going to lie about this situation. To win the Champions League is huge for everyone.
Kane was also in action on Sunday, but found little joy as Manchester City kept him quiet during their 3-1 victory at Wembley.
That takes Kane to within four goals of Salah, who has 29 in the league for Liverpool after joining from Roma in the summer.
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"I care about the goal because it provided us the three points but all that happens after is more players' decisions or the club's decision", he added.
"I don't believe. I don't believe", he said.
"But you know, you can see [against Bournemouth] with the team everyone tries to pass the ball to me to help me".
Two-time reigning Golden Boot victor Kane has been criticised after he was awarded Tottenham's second goal from their 2-1 victory over lowly Stoke City in the Premier League last week.
And he also says Kane never thought he would be open to such ridicule when trying to get the goal.
"[Salah] told me he's going to claim all of them", Henderson told BT Sport after his team-mate netted his 30th top-flight goal of a remarkable campaign. If it was me and I touched the ball I would try and claim it as well!