Harry Redknapp fielded a largely second string team, but with Luka Modric, Aaron Lennon and Jermain Defoe in his starting XI will be disappointed with the result.
First half goals from Dimitris Salpigidis and Stefanos Athanasiadis gave the visitors a first half lead, before Konstantinos Stafylidis was sent off for handling on his goal-line.
Luka Modric converted the resulting penalty, but the White Hart Lane outfit could not break the Eastern European team’s resolve in the second half, even with a man advantage.
Spurs are three points behind Rubin Kazan in Group A of the tournament, and must hope that PAOK beat the Russian in their last game of the pool, whilst Tottenham need to overhaul a five goal deficit against Shamrock Rovers.
Redknapp was not convinced of his team’s chances of doing this, and was disappointed with the showing against the Greeks.
“I am disappointed now because we are not going to be in the last 32,” Redknapp told The Daily Mail.
“It’s very slim – it is very difficult now. I wanted to stay in the competition but it wasn’t to be. Full credit to the opposition, they worked hard and looked dangerous.
“We started sloppy and didn’t defend well. It was a new back four and for the first 10 minutes we started like we did not know each other.
“The kid handballed it on the line and we made it 2-1 and at that point I thought we would come back and win it, but they got bodies back and it was difficult,” he concluded.
Spurs will look to bounce back from the defeat against Bolton in the Premier League on Saturday at White Hart Lane.
Meanwhile Birmingham and Celtic also were beaten in the competition, with Braga and Atletico Madrid claiming victories over the English and Scottish sides.
By Gareth McKnight