The hosts earned a crucial win, largely thanks to a brace from the Belgian forward, to give their survival hopes a huge boost with just three league games remaining
The Belgian has been revitalised following Tim Sherwood's arrival in February, and was at the double before the break to help move Villa into 14th - albeit still only two points clear of the bottom three after Sunderland also won on Saturday.
Benteke scored at either end of the first half to earn the FA Cup finalists a two-goal lead that their dominance deserved.
Roberto Martinez's Everton - lacklustre prior to the break - were afforded a way back into the game when Romelu Lukaku joined his compatriot on the scoresheet with a penalty before the hour mark.
However, Tom Cleverley scored for a second week running just five minutes later to further bolster Villa's survival hopes and leave Martinez scratching his head.
Everton, so positive in their 3-0 win over Manchester United last time out, were undone by a confident Villa side despite a scrappy late header from Phil Jagielka.
Both sides started relatively slowly despite promising recent form, but Benteke glanced an early header wide before going one better soon after.
The excellent Fabian Delph's looping cross found the Belgian, who held off Jagielka and John Stones to head home his seventh goal in six games.
The returning Charles N'Zogbia tested Tim Howard soon after as Villa continued to enjoy the upper hand.
Aston Villa gave Shay Given his first top-flight appearance in almost three years but the Irishman was barely troubled in the first 45 minutes as Everton failed to muster an effort on target.
Benteke again made the most of slack defending on the stroke of half-time as he lost his marker and converted Ron Vlaar's knockdown at the far post.
Lukaku took advantage of space in the Villa ranks to threaten with a strike shortly after the restart.
The Everton striker continued to cause problems before the hour as his meandering run led to chaos in the area, with Vlaar felling Naismith - allowing Lukaku to give the visitors hope from the spot.
That was short-lived however, as Cleverley latched on to Leandro Bacuna's delightful pass to restore Villa's two-goal cushion, the midfielder clipping the ball past Howard.
Jagielka nodded in a second Everton goal from close range in stoppage time, amid suspicions of a foul by Seamus Coleman on Given, but Villa deservedly claimed the points to dent the visitors' top-half aspirations.