Only a 74th minute penalty from skipper Gareth Barry rescued Villa, who had appeared to be heading for their first Premier League home defeat since December 8 when beaten they by Portsmouth.
Middlesbrough, who last won away at Portsmouth on December 29, had seemed to be on course for a much needed win following a superb first-half strike from Stewart Downing.
After their FA Cup exit at the hands of Cardiff City, record signing Afonso Alves - still to score since his £12million arrival from Herenveen - was not even included in Middlesbrough's squad.
But Boro appeared to be up for their task more than Villa in the opening half hour and this was demonstrated when Mohamed Shawky rounded a couple of defenders before the ball ran into the patch of Mido, who guided his shot wide of the post.
However, the north-east club were encouraged by their promising start and cashed in on some indifferent Villa defensive work in the 23rd minute when Zat Knight made a poor clearance straight to Downing.
Knight attempted to redeem himself by racing back into the middle, but the damage had been done as Downing glided past the Villa defender to slot home his seventh goal of the season.
Villa's performance continued to deteriorate and seven minutes before the break Shawky went very close to increasing Middlesbrough's lead with a swerving shot just wide of the upright.
In the 43rd minute, John Carew had an effort cleared off the line by Mido and, from the rebound, he headed over the bar from close range.
Mido himself wasted a glorious opportunity early in the second half to increase Middlesbrough's lead when he casually flicked his shot over the bar.
Marlon Harewood was drafted in by Villa but the Midlands club were still very much off colour as Middlesbrough commendably defended their slender lead against some persistent home attacks.
Following a poor first half, Ashley Young came alive in the second period.
Luke Young was certainly alive to the danger but in the 74th minute he handled in the area and Barry converted the spot-kick to the relief of manager Martin O'Neill.
It appeared a harsh decision but it let Villa off the hook on a night when they were well below form against a Middlesbrough side which often played with more attacking flair.