We were made to pay for a stuttering start as Mark Kitching scored a basic opener for the visitors early in the game and, after Joe Wheatley struck a second for Boro three minutes into the second period, we had it all to do.
Miller pulled one back with a fine finish after good work by Shayon Harrison but, despite ending the game in the ascendancy, we couldn't force a leveller.
Goalkeeper Luke McGee came into the side and played 90 minutes, as did Josh Onomah and Harry Winks, but a lack of available defenders forced Under-21s Coach Ugo Ehiogu to deploy three central midfielders in the back four along with Christian Maghoma.
It was a frustrating first half from a Lilywhite perspective and it took a good 20 minutes for us to find any sort of rhythm in our passing.
Indeed, after Anton Walkes' early half-volley had goalkeeper Joe Fryer scrambling down to his right to shepherd it behind, the visitors took an eighth-minute lead when Callum Cooke set Tom McAloon free in the right channel and his low ball across the box wasn't dealt with, affording Kitching the simplest of tap-ins at the back post.
Onomah's rising shot from wide on the left curled away from the target on 17 minutes as we struggled to impose ourselves on the game and as the half went on there continued to be a lack of real chances at either end.
McAloon did knock the ball down to Arnel Jakupovic but he swivelled and shot over the top just beyond the half-hour mark while a dangerous Miller corner dropped close to the penalty spot but nobody in a Lilywhite shirt was on the end of it.
Then came our clearest opening of the first period as Emmanuel Sonupe found Harrison in the box from the right wing, the forward produced a great first touch before striking sweetly towards goal but Fryer got down low to make a fine save on 39 minutes. Winks felt he was impeded as he went for the rebound but the referee didn't heed his protestations.
Jakupovic's fierce 22-yard free-kick just cleared the crossbar on 42 minutes but his side doubled their lead three minutes after the restart as Cooke rolled the ball across from the right and Wheatley ran onto it at the edge of the box, striking low through a crowded area and into the bottom corner.
We almost produced an immediate response as Onomah's angled effort was steered over by Fryer and Maghoma stormed in to meet Miller's resulting corner but scooped over at the first time of asking.
Now attacking with greater urgency, Winks' curler was comfortably caught by Fryer before we made it 2-1 on 59 minutes with a very well-worked goal. Harrison took a couple of classy touches to keep the ball under control as he danced down the left side before sliding it forward for Miller, who sped in behind and finished clinically with his left foot from the angle.
That was as good as it got, though, as Cooke dragged wide of the far post for Middlesbrough while the same player struck a fierce free-kick straight into the grasp of McGee midway through the second half.
Parity was almost restored on 68 minutes when substitute Marcus Edwards stood the ball up at the near post for Miller, but his close-range header was clawed away by Fryer.
Two minutes later, Cooke found space down the right for Boro and squared for Jakupovic, unmarked in the box, but the retreating Filip Lesniak just did enough to put the striker off and we cleared our lines.
Miller's effort struck a defender but spun just the wrong side of the post as we continued to look for an equaliser and, after McGee's low save prevented McAloon from extending Boro's advantage, we made a real go of it in the latter stages with Edwards taking players on at will and Harrison and Miller looking to find the slightest of openings in the box, but it wasn't to be and the points went back to Teesside.
Spurs U21s: McGee, J Pritchard (Goddard 77), Stylianides (Edwards 58), Lesniak (c), Maghoma, Walkes, Sonupe, Winks, Harrison, Onomah, Miller. Substitutes (not used): Oduwa, McDermott (GK).
Middlesbrough U21s: Fryer, Johnson, Burn (c), Morris, McGinley, Tinkler, Cooke, Wheatley, Jakupovic, McAloon, Kitching. Substitutes (not used): Maloney, Tavernier, Curry, Jowers, Pears (GK).