After two disappointing defeats at Wembley, Spurs turned it around in their final Group E fixture after conceding to the Russians after 33 minutes.
Alan Dzagoev gave CSKA the lead when he latched onto a perfectly placed knockdown header from Zoran Tošić to fire beyond Hugo Lloris.
The contest was wrapped up in the 77th minute when CSKA goalkeeper Igor Akinfeev got a full hand to Alli's close-range header only to see the ball bobble its way into over the goal-line.
It was a thoroughly deserved win from Mauricio Pochettino's side who had more than 20 attempts on goal and close to 70% possession in what was a dominant performance.
The result sees the North Londoners finish third in their group with seven points from their six matches, allowing them to drop down into the Europa League Round of 32, with AS Monaco and Bayer Leverkusen finishing first and second.
2016/17 UEFA Champions League - Group E