It was Spurs' fifth straight home win in the Premiership and still leaves Gareth Southgate's men without maximum points on their travels for nine months.
Martin Jol's side showed early on why their record at White Hart Lane has been so impressive this season with a flurry of early opportunities - all of them falling to Jermain Defoe.
After seeing a well-struck free-kick whistle over the bar on 16 minutes, he found himself with the goal gaping twice in the space of three minutes.
On 18 minutes, strike-partner Dimitar Berbatov showed brilliant skill to take down a high ball, turn and slide the England striker clean through, but Mark Schwarzer did well to keep out his fierce shot.
Defoe did not have to wait long until he was in again, this time thanks to Steed Malbranque, but once again he failed to take his chance a scooped an effort over the bar from ten yards.
And his side were nearly made to pay just over ten minutes later when Boro defender Emanuel Pogatetz put a free-header inches wide from a Stewart Downing corner.
However, Spurs finished the half much stronger than their opponents and Schwarzer was called into action once again five minutes from the break when he had to tip over a stinging Tom Huddlestone shot from the edge of the box after Abel Xavier had half-cleared an Aaron Lennon cross.
A goal was coming for the home side and they had to wait just three minutes into the second half for it to come.
And it was yet another masterpiece from £10.9m summer-signing Berbatov, who netted his seventh goal in Spurs colours.
Huddlestone fizzed a free-kick across the box where Pascal Chimbonda did well to out-jump his taller marker. The header was met on the volley by the Bulgarian and the ball looped beyond Schwarzer into the far corner.
His third Premiership goal brought his tally level with Defoe's, who was having no luck in this game.
He was put clean through again by Didier Zokora on 55 minutes, but the brilliant Jonathan Woodgate raced back to deny him just as he was about to pull the trigger.
However, Boro gave a timely reminder just after the hour mark when a fierce Robert Huth free-kick forced Paul Robinson into his first save. Spurs failed to clear and substitute James Morrison hit a shot wide when Xavier put the ball back in the box.
This proved to be an early warning for what was to come, for although Defoe was denied twice more by Schwarzer, Spurs' inability to clear their lines at the back nearly cost them.
With ten minutes left on the clock, Downing's corner was headed up in the air by Chimbonda, only for Pogatetz to head down and Huth to slam home for what seemed an undeserved point.
But just as the goal went in, Jol threw on his trump card – last season's leading scorer Robbie Keane.
And it took just three minutes for him to latch on to a quick Huddlestone free-kick and pick his spot from 20 yards to give Spurs all three points.
However, a fracas between Zokora and George Boateng two minutes from time in which hands were raised marred the game and both were sent off.