Alli, 20, held off competition from Kane, Stoke City goalkeeper Jack Butland, Liverpool midfielder Philippe Coutinho and Everton duo Romelu Lukaku and Ross Barkley to take the young player gong.
Alli, who won Football League Young Player of the Year 12 months ago, joined Tottenham from third-tier Milton Keyes Dons in 2015 and was expected to be used sparingly in his first season at White Hart Lane.
However, he has been outstanding in midfield for Spurs and has already won six caps for England, scoring once.
He was not there to pick up his award in person as Tottenham play West Bromwich Albion in the Premier League on Monday, but recorded a video message.
“Sorry I can’t be there tonight, but we have a big game tomorrow. Thank you for to everyone who voted for me,” Alli said.
“I feel honoured to win such a prestigious award and thank you to my friends, family and all the staff at Tottenham.”
Manchester United great Ryan Giggs, now the assistant to manager Louis van Gaal, followed in the footsteps of his former manager Alex Ferguson by winning the PFA Merit Award.
Manchester City midfielder Izzy Christiansen won the PFA Women’s Player of the Year award, with Sunderland forward Beth Mead taking home the young player equivalent.
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