A goal from former Bolton forward Rodrigo and a brace from captain Luisao gave the visitors a strong lead despite Christian Eriksen's superb free kick.
A second defeat in a matter of days all but ended Tottenham's hopes of progressing in the Europa League.
Below are the Spurs player ratings from the match:
Hugo Lloris 6/10 - Wasn't overly threatened early on, Benfica scored with their only shot on goal in the first 35 minutes, an effort the Frenchman didn't really have a chance with. But throughout the second half looked anything but reliable. One risky excursion out of his box to mop up some sloppy defending was followed by an even crazier moment when he had to dive backwards to slap the ball out for a corner after running out of his area. Palmed Garay's header into the path of Luisao for the third, with the Brazilian smashing in his second goal of the game.
Kyle Walker 6/10 - Made a super sliding challenge that then set Lennon free down the right, but was kept on his toes against a Benfica team full of their own pace. Withdrawn for Danny Rose with 15 minutes left, with Naughton moving back out to the right.
Kyle Naughton 5.5/10 - Was guilty of giving Rodrigo far too much space for his goal, leaving him unable to challenge the former Bolton loanee. Some decent moments as he pushed up more in the second period, but left the backline exposed by doing so.
Younes Kaboul 6/10 - Captain for the night as Michael Dawson missed out through injury. Challenged back-up keeper Jan Oblak early on from a free kick, being somewhat unlucky to concede a free kick after a decent leap. Made a couple of excellent challenges as he stepped out of defence. Lost Luisao at a corner for the Brazilian to nod home unchallenged, and also left the Benfica captain free to smash in Benfica's third. For much of the game played well but switched off at key moments.
Jan Vertonghen 6/10 - Vertonghen had a fairly comfortable evening until the last 30 minutes, with Benfica preferring to counter down the wings with their pace rather than attack the centre of the Tottenham defence. Like Kaboul, stepped up well to seize the ball on more than one occasion, but late one failed to stop the Spurs defence being repeatedly stretched. Booked for a heavy challenge on Nicolas Gaitan.
Sandro 6/10 - The Brazilian received a booking early on for taking out Miralem Sulejmani as Benfica looked to counter. The Beast also screwed a shot wide at the end of a neat move involving Lennon and Eriksen. Some of his passing was a little loose, though the side were weaker once he was withdrawn.
Paulinho 6/10 - Made one wonderful cushioned lay off after pushing forward to challenge a Benfica man. Also guilty of a sloppy pass that gifted possession to Markovic. Employed some tenacious play to break past Benfica's midfield line before handing possession over to Christian Eriksen. Went missing for the last 25 minutes.
Christian Eriksen 6.5/10 - Eriksen was one of the busier players on the pitch, often getting on the ball from his inside left position. He didn't really orchestrate the game in the way he would have liked, with his final ball and set pieces a little disappointing. Early in the second half, he and Paulinho brought the ball forward and the Dane played a great ball through to Adebayor. Another fine piece of interplay with Kane gave him the chance to score another exquisite free kick - his third this season.
Aaron Lennon 6/10 - Looked much more dangerous back on the right hand side and gave Guilherme Madalena a difficult game. Dribbled infield at one point only to weakly shoot at Oblak with his left. Drifted from the game late on.
Harry Kane 6/10 - To begin with it looked like Tottenham would benefit from having two physical men to aim for up top as Kane started for just the second time this season. As it turned out, Kane was sat too deep to impact offensively often leaving Adebayor isolated when balls were played up to him. Started the second half a little better with one moment of great control before releasing Lennon, but then was guilty of dawdling on the ball, gifting Benfica a chance, and then the corner, for their second goal. Linked up well with Eriksen to win the free-kick for the Dane's goal.
Emmanuel Adebayor 5.5/10 - Tottenham's form player failed to bully the Benfica defence facing him, with several passes forward being won by the impressive Luisao. Adebayor was a willing battler, just lacking that break, not to mention some support from his teammates. The one good chance he had early in the second half, he shot tamely wide.
Roberto Soldado (75') 5.5/10 - Saw very little of the ball once he came on, as Benfica showed their class to continue to threaten on the counter.
Danny Rose (76') 6/10 - Made his return from injury after coming on for Kyle Walker for the last 15 minutes, and struggled to adapt to the pace of the game.
Nabil Bentaleb (82') 6/10 - A late substitute for the tiring Sandro.