Boateng, who also won the 87th penalty converted by Yakubu, exploited Villa's defensive problems to pave the way for only Boro's third Premiership win of the season.
On the strength of Villa's latest defeat they are destined to be heading for a difficult season as this is now their worst ever start in the Premiership.
During the interval Villa's old stars paraded the European Cup they won in 1982 but on current form there appears little likelihood of any silverware being won this season.
Middlesbrough made four changes from the side which progressed in the UEFA Cup against Xanthi and manager Steve McClaren was obviously delighted with the outcome against Villa.
They had previously only won one of their last nine games following a European tie and that solitary success was against Villa last season.
As expected, former Villa stars Gareth Southgate and, in particular, Boateng were again key players for Boro.
Southgate gave Juan Pablo Angel little scope of ending his barren run of failing to score for Villa this season. He has now gone seven games without a goal and this is reflected in Villa's indifferent displays.
There was little penetration despite the fact that Villa were always prepared to move forward.
Middlesbrough, on the other hand, often conspired to cause panic in Villa's rearguard. Yakubu was a potential threat. In the opening minute he turned Olof Mellberg and forced Thomas Sorensen to make a good save.
Sorensen was again in action saving from Szilard Nemeth, while Villa's defence found itself in a terrible tangle keeping out Boateng when the ball eventually ran loose for Yakubu to shoot wide.
Yakubu, however, took full advantage of Villa's fragile defence when a cross from Fabio Rochemback was headed to the Boro striker by Wilfred Bouma.
His weak goal attempt was pushed back to him by Liam Ridgewell and the former Portsmouth striker made no mistake to put Boro ahead in the 33rd minute.
Only a brave save by Sorensen prevented a second goal from Rochemback, while Villa's best attempts came in successive attacks when Angel and Luke Moore headed attempts just over the bar.
Moore turned out to be Villa's saviour as he put them back into the game with a 50th minute equaliser after Patrik Berger's shot had bounced off Angel into his path.
Berger then hit a shot on the run against Boro's post in a bid to gain the upper hand following their indifferent first-half performance.
But Villa were stunned in the 64th minute when Boateng took particular delight in grabbing the second goal against his old club. A right-wing corner from Rochemback wasn't cleared and the ball found its way to the lurking Boateng who hammered his shot past Sorensen.
Three minutes from time Boateng was brought down just inside the penalty area by Jlloyd Samuel to cap Villa's tale of woe.
Yakubu calmly converted the spot kick to send Villa's fans streaming for the exits.
They missed Steve Davis scoring in the last few seconds of the game with a powerful drive but by then it was far too late to make any difference to the outcome.