The Belgium striker, revitalised since Tim Sherwood’s appointment as manager in February, scored twice in the first half for the FA Cup finalists to take his tally to 11 goals in nine games.
His international colleague Romelu Lukaku reduced the arrears with a penalty, but Tom Cleverley struck what proved to be the winner, with Phil Jagielka hitting back for Everton at the death.
Following victory in the 200th staging of the English top flight’s most-played fixture, Villa remain two points above the relegation zone, with Everton slipping to 11th place after a first defeat in seven matches.
Sherwood handed Shay Given a first league start since 2012, with Brad Guzan dropping out, but the veteran Ireland goalkeeper had little to do in the first half as the home team completely dominated.
Jack Grealish, Villa’s 19-year-old forward, had garnered glowing praise for his performance in the 2-1 FA Cup semi-final victory over Liverpool and his dead-ball prowess provided the bedrock for the hosts’ success.
After Grealish had troubled Everton with a corner that narrowly eluded Benteke and Ron Vlaar, Benteke made the breakthrough in the 10th minute by out-jumping Leighton Baines to head home Fabian Delph’s left-wing cross.
Villa continued to apply pressure and after Tim Howard had repelled a long-range Charles N’Zogbia free-kick and Vlaar had come close to converting a corner from Grealish, they doubled their lead on the stroke of half-time.
Grealish was again the architect, whipping a corner into the box from the left, and Vlaar’s flick-on enabled Benteke to steer the ball into an empty net at the far post.
Everton did not muster a single shot on goal in the first half, but they rectified that statistic within three minutes of kick-off in the second period.
Lukaku drew a save from Given with a low effort after breaking clear and then got in front of Benteke to head over from the subsequent corner.
Shortly before the hour, Lukaku gave Everton a lifeline from the penalty spot, squeezing a shot past Given following a staggered run-up, after Vlaar clumsily felled Steven Naismith.
But against the run of play, Villa restored their two-goal advantage when on-loan Manchester United midfielder Cleverley emphatically converted Leandro Bacuna’s fine through-ball to register his second goal in a week.
Visiting captain Jagielka headed home from close range in injury time, but by then it was too late.
Mark Noble pushed Burnley to the brink of relegation from the Premier League as the West Ham midfielder’s penalty sealed a 1-0 win over the 10-man Clarets on Saturday.
Sean Dyche’s team had defender Michael Duff controversially sent off midway through the first half at Upton Park and Noble converted the resulting spot-kick to condemn the visitors to their fourth successive defeat.
Burnley remain rooted to the bottom of the table, eight points from safety with only three matches left, and look certain to suffer a quick return to the Championship just 12 months after their promotion.