The only goal in the 69th minute of this quarter-final tie took a wicked deflection to leave Paul Rutherford helpless as the ball nestled into his opposite corner.
To add insult to injury, defender David Tyrie's 'goal' in the last minute was disallowed for a handball spotted by the linesman.
It was harsh on the lads after they'd completely dominated the first hour at the Riverside Stadium.
In that time home keeper Ross Turnbull saw regular action and made two telling saves while Rutherford was a spectator for long periods.
We were by far the better side in the first half and enjoyed long spells of possession, fizzed the ball around on the slick surface and created the better chances.
Jamie O'Hara impressed with his range of passing in midfield, Mark Yeates buzzed about typically and Marcel McKie was a constant threat down the left flank.
At the other end another solid defensive performance made sure Rutherford wasn't tested.
The same couldn't be said of home keeper Turnbull. He produced a stunning save to turn aside Lee Barnett's 20-yarder in the 25th minute and was there again to block from Yeates as the impish midfielder burst into the box from Phil Ifil's slide-rule pass just before the break.
In-between those key efforts, Michael Malcolm flicked McKie's cross just wide, O'Hara stung Turnbull's fingers from distance, Yeates was a yard heavy with a pass that would have sent Jamie Slabber clear and Slabber couldn't quite get the power on a header from Barnett's cross.
Suffice to say, the home side would have been pleased to go in at half-time on level terms.
The second half started in a similar fashion with Spurs on top and it took just five minutes for the first chance to arrive as Danny Foster headed Yeates' corner wide from eight yards.
But Middlesbrough, who had managed just one shot on goal, then took the lead thanks to a massive slice of luck.
With 69 minutes on the clock James Morrison ran at the defence and his shot from 25 yards took a huge deflection to leave Rutherford stranded.
Owen Price and Nicky Wettner entered the fray as Pat Holland went in search of an equaliser and as the game became more and more stretched, Rutherford was forced into action twice in a minute.
Time ticked away but there was one last chance as Tyrie suddenly found himself in the clear at the far post.
He controlled the ball and volleyed in off the post only for celebrations to be cut short but the linesman's flag.
Line-ups: Middlesbrough: Turnbull, McMahon, Harrison, Bates, Wheater, Liddle, Peacock (Craddock, 67), Taylor, Kennedy (Nordgren, 45), Morrison, Brunt. Subs: Knight, Reed, Masters.
Spurs: Rutherford, Ifil, McKie (Wettner, 76), Tyrie, Foster, Dobson, Barnett, Malcolm (Price, 69), Slabber, Yeates, O'Hara. Subs: Black, Eyre, McKenna.
A huge slice of misfortune saw our Academy side knocked out of the FA Youth Cup at Middlesbrough on Thursday night.