The Boro side showed four changes from that which lost away to Wolves seven days ago with Carlos De Pena making a rare appearance at this level.
Matthew Elsdon was favoured ahead of Niall McGoldrick, while elsewhere Bryn Morris, Marcus Tavernier and De Pena replaced Mark Kitching, Jo Wheatley and Alex Pattison.
Villa made a flying start and in the opening seconds a left wing cross flew through the Boro box and just evaded Corey Blackett-Taylor who arrived at the back post but couldn't get the touch he was looking for.
It was nine relatively chanceless minutes later when De Pena delivered a cross from the left. The merits of whether it was intentional of not can be debated, irrespective of whether it was or not it deceived Viktor Johansson.
Boro's play on what looked in places an uneven surface was neat and a step up on the performance delivered away to Wolves last week. It was the direct approach, though, that almost brought a breakthrough.
Attacking through the middle after an ambitious overhead kick from Rushian Hepburn-Murphy was well off target, a controlled move picked out Tavernier 22 yards from goals. Johansson couldn't hold the shot and Arnel Jakupovic tucked in. There was no time for celebration however, as a linesman's flag ruled out the effort, offside the call.
A long ball sent Joao Morelli off in chase towards the left-hand edge of the Villa box. A whipped in cross from the Brazilian was only just ahead of Jakupovic as Boro threatened once more.
Andre Green missed a chance to at least get a shot on target when shooting well over and Boro broke to win a corner and take the lead.
A combination of slack marking and a well-timed run allowed Carlos De Pena time to power in a header from right-wing corner with 38 minutes played.
It was very nearly two just two minutes later but Callum Cooke delayed a shot just too long and Johansson spread well to save shorty before Hepburn-Murphy rattled the bar with a powerful shot from 30 yards.
Half-time Middlesbrough U23s 1 Aston Villa U23s 0
Boro started the second half brightly enough and Joao Morelli forced Johansson into two saves following good approach work, the second a smart one low to his left to tip round for a corner.
In between the saves Villa drew level as, with 51 minutes played, Green advanced down the left and crossed low. The delivery should have been dealt with. It wasn't, Boro made a mess of it and Keinan Davis was left with a simple tap in.
The self-destruct button was pressed again 14 minutes later when Jordan McGhee tripped Khalid Abdo inside the penalty area and the midfielder, following a stuttering run-up, sent Aynsley Pears the wrong way from the spot.
It was almost three when Hepburn-Murphy sped away down the left and despite having his shirt tugged managed a low cross which flew inches wide.
The same player curled just wide from 20 yards before Junior Mondal, on for Morelli and picked out with an inch-perfect pass, wasted good approach work when blasting well over.
Jakupovic was next to clear the bar, from 16 yards, as Boro pressed for a late equaliser and were denied for the final time when, after a tricky run down the right from Mondal, Jakupovic had a shot on the turn blocked.
Scorers De Pena 38, Davis 51, Abdo (pen) 65
Middlesbrough: Pears; Johnson, Elsdon, McGhee, Morris (Capt. from 66), Tinkler (Capt. to 66) (Pattison 66), Morelli (Mondal 70), Tavernier, Jakupovic, De Pena, Cooke. Subs: Fryer (gk); McGoldrick, Wheatley.
Aston Villa: Johansson; Hale, Leggett, Lyden (Abdoul 61), Sundman, Abdo, Blackett-Taylor (Linley 82), Davis (Hayes 77), Hepburn-Murphy, O'Hare, Green. Subs: Idem.
Referee Martin Coy
Boro Johnson 59, foul; Jakupovic 72, foul.
Villa Hepburn-Murphy 84, ungentlemanly conduct.
Conditions Cold and damp