Norwich winger Robert Snodgrass saw his sixth-minute spot-kick saved before the visitors lost Benteke to injury, with his replacement Libor Kosak scoring the only goal in a 1-0 win for Lambert's side.
It was a first Villa goal for towering Czech Republic forward Kosak and it gave Lambert another victory at the home of his former employers with whom he spilt so acrimoniously after guiding them to the Barclays Premier League from League One in two years.
Lambert has now won on all three of his returns to Norfolk and the Scot also saw his side keep their first clean sheet in the league since December 8.
His replacement at Norwich was Chris Hughton, who had said before the game that he was looking for a reaction from his players following defeat at Tottenham last weekend but, other than a dominant spell in the first half, they did not put in the sort of performance that warranted three points.
It was a very open first 15 minutes, starting when Andreas Weimann wriggled his way through inside the first 60 seconds but stabbed an effort straight at John Ruddy.
The Austria international again found himself in plenty of space two minutes later, this time his curling effort beat Ruddy but came back off the post, with Benteke flagged offside as he looked to tuck away the rebound.
But it was the home side who spurned the best opportunity of the frenetic opening stages when Snodgrass passed up the chance to open the scoring from the penalty spot.
Nathan Redmond's deep cross was headed back across goal in towards Ricky van Wolfswinkel and struck the arm of the recalled Ciaran Clark with referee Chris Foy immediately pointing to the spot.
Snodgrass struck a hard penalty but Brad Guzan flew to his left to push the ball away and keep the game scoreless.
Norwich again missed a fantastic chance on 12 minutes as Redmond pulled Snodgrass' cross back in to the danger area but Van Wolfswinkel could only throw his chest out towards the ball and direct it behind for a goal-kick.
The home side remained on top as Snodgrass and Redmond enjoyed relative success down either flank, although Villa showed when they countered that they held their own attacking threat.
Christian Beneteke's goalbound effort was deflected behind by Michael Turner before captain Ron Vlaar's acrobatic effort from a corner flew wide.
The Belgium forward then required treatment after an awkward landing and, despite coming back on, he was again struggling.
Whilst Benteke was grounded Norwich came close to opening the scoring as Van Wolfswinkel rifled a shot just inches wide of Guzan's post.
Kozak then replaced Benteke and needed just two minutes to put the visitors ahead.
The summer signing from Lazio saw a close-range shot saved by Ruddy but was on hand to force home Gabriel Abgonlahor's resulting cross.
The England goalkeeper then had to punch away a ball across his goal by the lively Agbonlahor as the Norwich fans began to vent their frustrations at their side's inability to hold on to possession.
The Canaries' problems worsened as captain Sebastien Bassong was forced off with what appeared to be a leg injury, with Ryan Bennett replacing him at centre-back.
The second half did not start with the same vigour as the first and there was not really a note of chance until Weimann bent an effort wide of the post with 52 minutes on the clock.
Gary Hooper was introduced for his Norwich debut, with the summer signing receiving a rousing reaction from the home crowd, who then turned on Hughton when Redmond was hauled off for Anthony Pilkington.
Leroy Fer flashed a cross low in to the Villa box that just eluded the on-rushing van Wolfswinkel as Norwich still struggled to test Guzan and his defence on a regular basis.
Neither side could get a stranglehold on possession and it was Villa who created the next chance as Clark headed Leandro Bacuna's corner just wide of Ruddy's post.
Kozak came close to a second goal as Villa caught their hosts on the counter attack but his 77th minute strike was deflected behind by Turner.
The home side continued to commit more and more players forward and it was Van Wolfswinkel who was next to see a goalbound effort turned behind for a corner.
Guzan was again the hero for Villa as he acrobatically tipped over a Hooper shot in the closing stages after the former Celtic striker had failed to truly connect with Javier Garrido's cross.
Lambert's side then saw it the five minutes of added time without much incident to secure their first points since their opening day win at Arsenal.