The game was a dead rubber for Spurs, with progression as group winners already sealed before a ball had been kicked, but there was still pride to play for.
Towering frontman Fernando Llorente went into the game with a point to prove, having yet to score since joining the club from Swansea in the summer.
The 'Lion King' took his chance, putting the hosts in front after 20 minutes with a lovely swivel and finish to net his first goal for the club on his 17th appearance.
The former Athletic Bilbao man was also involved in Spurs' second, teeing up Son to stroke the ball past a helpless Nauzet Perez from the edge of the box.
The South Korean was at the heart of much of the hosts' best play in the first half, though the visitors did threaten briefly after the break.
Striker Mickael Pote fluffed his lines twice, before Llorente contrived to miss the ball with the goal gaping.
The icing was put on the cake late on though as Georges-Kevin N'koudou saw his effort deflect past Perez and into the net as Spurs matched the result from the reverse fixture in Cyprus.
All in all it was a successful evening's work for Spurs, who end the group stage having claimed 16 points from a possible 18 from a group containing both Real Madrid and Borussia Dortmund, something that will no doubt delight Pochettino, even if their league form leaves plenty to be desired.