The Teessiders are still looking to clinch their highest ever top-flight finish and picked up three points against a City side that can be thankful they are already effectively safe from the drop.
The first goal of the afternoon was a testament to the trickery of Massimo Maccarone and a large slice of luck.
The Italian was set free down the left by Bolo Zenden and - after slipping past Richard Dunne - he saw his attempted cross slice into the net with David James left stranded and in shock.
The goal had been on the cards after the hosts had started the game eager to give their fans a final home game worth remembering through the summer months.
Almost immediately after the hosts had broken the deadlock, they were on the attack again. Danny Mills was given the freedom of the right-hand side by the Citizens rearguard and his cut back from the byline allowed George Boateng to hammer an effort on target that James did well to hold.
However the second goal was not long in coming as Szilard Nemeth reacted the quickest to Joseph-Desire Job's knock down to poke the ball home and double Boro's advantage.
City did not appear likely to get back into this game until some slack play from their opponents allowed them to pull a goal back.
Gaizka Mendieta dwelt on the ball for too long and was robbed of possession by Paul Bosvelt. The Dutchman passed the ball on to Paulo Wanchope and the Costa Rican left Danny Mills bamboozled with his skills to allow him to slot home past Mark Schwarzer with his left foot.
The goal clearly galvanised Kevin Keegan's men and - with vocal support from their ever-faithful supporters - they went about finding an equaliser before half time.
They would have done so had it not been for the referee's whistle as the official disallowed Joey Barton's effort after he had apparently fouled Schwarzer as they challenged for a high ball.
The interval took some of the cohesion out of the game and the second half sadly lacked much of the decisive attacking play that had been on display before the break.
Nemeth and Nicolas Anelka both tried their luck from the edge of the box but failed to test the keeper as some hefty tackling and loose passing disrupted the flow of any rare bright moments.
City did have a glorious sight of goal in the final 15 minutes but substitute Stephen Elliot made a mess from eight yards out after Shaun Wright-Phillips had robbed Zenden on the right to cut the ball back to him.
The Citizens may have effectively secured their Premiership status but Keegan has a lot of work to do in the summer and he could do no worse than take a look at his opposite number who has built a solid team always willing to fight hard for precious league points.
