Spurs clinch place to next round
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Needing just a draw to progress, Spurs had an air of complacency about them in the opening period, which Panathinaikos controlled for large parts.
Emmanuel Adebayor put Tottenham ahead just before the half hour, but the Greeks, who have never won in Britain, played the better football and deservedly equalised through Zeca just after the re-start.
Panathinaikos, knowing victory was their only means of qualifying for the knockout stages, threw everything at Tottenham and looked the more likely to score before Clint Dempsey - whose shot went in after hitting both the bar and keeper Orestis Karnezis - and Jermain Defoe settled the game late on.
First Dempsey's header home Kyle Walker's cross made it 2-1 and Defoe killed the game off with his 13th goal of the season with seven minutes left.
It was hardly Tottenham's most vintage performance of the season - and the game itself was largely poor in quality - but Andre Villas-Boas will sleep easier tonight knowing his team are one step closer to lifting the cup that he won with Porto in 2010.
Lazio's drubbing of Maribor means Villas-Boas' men qualify second from Group J, with a potential Champions League drop-out awaiting them in the second round.
The raucous chanting from the travelling Panathinaikos fans provided the only entertainment in the opening stages as both teams started slowly on a bitterly cold night in north London.
Panathinaikos had only beaten an English team once in their history, but they looked the more likely to break the deadlock in the first 15 minutes.
Toche, whose goal earned Panathinaikos a point in the reverse fixture two months ago, sprinted on to an Ibrahim Sissoko through-ball, but he mis-controlled the pass and Brad Friedel gathered easily.
The Spaniard then slipped his marker to meet Giourkas Seitaridis' cross, but he could only shoot weakly at the Spurs stopper.
Spurs were struggling to get into the game and were missing the influence of Gareth Bale, who was absent due to a hamstring injury.
Like many of Tottenham's games in the Europa League, the contest was not proving to be the best advert for the competition, but all of a sudden Adebayor put the hosts ahead.
The Togo marksman spun off his marker to collect Dempsey's through ball and slot the ball past Karnezis after a cushioned touch.
Tottenham still struggled to get out of first gear despite the goal. Indeed, Panathinaikos came back at the Londoners through Toche, who beat the offside trap but Friedel raced off his line to claw the ball away.
Sandro and Defoe both cleared the bar with wayward shots as the half drew to a close and Tom Carroll then slipped in Adebayor, but his shot was blocked by Kostas Triantafyllopoulos.
Tottenham came out a bit brighter in the second half and were unlucky not to score their second three minutes after the re-start.
Dempsey fed Defoe with a clever pass, but the England striker's shot struck the foot of a post before bouncing to safety.
Panathinaikos then stunned the home side with a 54th-minute equaliser. Poor marking from Walker allowed Zeca to meet Nikos Spyropoulos' cross and he beat Friedel with a clinical header.
The 1,816 away fans rejoiced and Lazaros Christodouloppulos emerged from the bench to give the visitors an extra outlet up front.
The Greeks, willed on by their vocal support, continued to pressure Spurs, who were playing some of their worst football of the season.
Kyle Naughton's frustration got the better of him as he put in a rugby-style ankle tap on Sissoko to earn a booking.
Tottenham failed to clear a routine Panathinaikos cross and the ball fell to Toche, but he shot wide.
Jan Vertonghen put in a crucial header to clear Spryopoulos' wicked corner as the Greeks continued to pile on the pressure amid a tense atmosphere inside the stadium.
Dempsey then settled the home fans' nerves with Tottenham's second. Completely against the run of play, Sandro earned a free-kick 25 yards out after a foul by Zeco. Walker swung in a deep cross from the set-piece and Dempsey's header struck the bar before bouncing in off the keeper.
It proved to be Dempsey's last contribution to the game as he came off for Gylfi Sigurdsson. The American received a standing ovation from the home fans, but Villas-Boas instead decided to give the forward what looked like a tactical talking to on the touchline.
Any hopes of an unlikely Panathinaikos comeback were dashed with seven minutes left when Defoe latched on to Aaron Lennon's pass and chipped the ball over Karnezis.
The goals knocked the stuffing out of the visitors, but their fans continued chanting as a relieved Spurs team took their foot off the accelerator and claimed all three points.