Kane was the heavy favourite with the bookmakers to scoop the prestigious award after captaining England to the World Cup semi-finals while also winning the Golden Boot.
However, the Tottenham striker only came third in the standings when the British public voted this evening.
Tour de France winner Geraint Thomas came out on top as he crowned off a marvellous year with the SPOTY award.
Formula One star Lewis Hamilton came second after he secured his fifth world title this year.
But Thomas, who is an avid Arsenal supporter, along with Hamilton, was able to call on votes from his fellow Gunners fans as they were desperate to stop their north London rival’s key man getting his hands on the honour.
One supporter wrote on Twitter: “Arsenal fans voted for Thomas to get one over Kane because he is a Gooner..yes we would have done the same. This is why public voting needs to stop #SPOTY.”
And another added: “Arsenal fans voting for anyone but Harry Kane there #SPOTY.”
While a further tweeter noted: “Arsenal fans voting for Lewis Hamilton #SPOTY.”
Furthermore, another football fan wrote: “So Arsenal fans show our voting power again by getting a one two on SPOTY,” a fan wrote.
“Do s***s have any fans? They only had one man to vote for and we could have split our vote over our two. Goal of the season should be easy.”
And a further dig to Kane came from another user: “@GeraintThomas86 is a Gooner. @Arsenal beat the Spuds again. #northlondonisred #SPOTY.”
Thomas was overcome with joy as he beat Hamilton and Kane to the SPOTY award.
“It’s just insane now I am stood here. I think I have got so many people to thank,” he said after accepting the trophy on stage.
“I will obviously start with my wife. It is just as much for her as it is for me.
“She is always there and picks me up. I am really lucky to have her and my family.
“As a bike rider I always thought I am just focussed on myself. I keep hearing stories like Tyson [Fury] and Billie [Jean King] and you realise what we do inspires people back home.
“You can take just as much pride from that as winning something like this.”