This was their eighth draw of the season and reflects their shortcomings in front of goal.
Struggling Middlesbrough, who have yet to win away from home this season, were able to stay in contention and were well worth their point on the day.
The match was a real story-book return for Malcolm Christie who made his first appearance for 14 months and marked the occasion with his first goal since February 25, 2005 at Portsmouth.
It was certainly the highlight of the match for the unfortunate Middlesbrough striker who has suffered three broken legs in recent years.
But he made a confident return and his opportunist goal lifted Middlesbrough's spirits and in turn jolted Villa's victory aspirations.
Villa may have increased their unbeaten home record to seven games to keep themselves in a challenging position for a spot in Europe next season, but it was a performance which left some question marks about their ability to maintain their impressive start to the season.
Villa's morale has undeniably been lifted by O'Neill's influence, but their lack of goalscoring flair is still a major flaw in their make-up and urgently needs attention.
It became increasingly obvious that it was going to be very much a defence dominated battle on the part of Middlesbrough. They were often content to funnel back in their bid to contain Villa's eager attacks but later gained in confidence to put pressure on the home defence.
It was a somewhat dangerous policy but understandable in view of Middlesbrough's miserable away form after losing their last three away games on the road.
Abel Xavier was given his first outing since his 12-month ban imposed after he failed a drugs test. Ironically, his previous Boro appearance was in the corresponding game against Villa which the North-East club won 3-2.
Middlesbrough adopted a defensive operation in the opening stages which was hardly surprising in view of their dismal record on the road.
Robert Huth appeared to be well in command against the struggling Juan Pablo Angel and Middlesbrough appeared quite content to frustrate Villa.
Goal opportunities were rare with Isaiah Osborne wasting the best chance to put Villa ahead with a weak header, while young Gary Cahill missed from a couple of yards.
But a powerful 30-yard drive from Wilfred Bouma which was pushed around the post by Mark Schwarzer sparked the game to life in a hectic spell at the end of the first half.
Schwarzer brilliantly saved at the feet of Barry and immediately Boro launched the attack which ended in Christie putting Boro ahead against the run of play in the 41st minute.
There was a suspicion of off-side but it did spark off more robust play from Villa with Angel having a goal ruled offside.
Villa could not be denied and Stilian Petrov ghosted through only to be brought down by Schwarzer to concede a penalty which Barry rammed home.
It was Barry's third successful spot kick and Villa's eighth penalty award of the season and it could not have come at a more opportune time.
In the second period Villa often appeared to be the more dangerous with Olof Mellberg going close, while substitute Milan Baros, still off the pace, hammered a shot well wide.
Villa lost the services of goalkeeper Thomas Sorensen following a clash with Huth and they still failed to break down Middlesbrough's stubborn defence which promises a brighter future for the North-East club.