After a cagey first period, the Dutch outfit took a shock lead courtesy of Evangelos Pavlidis, however a pair of headed efforts from defender Diego Carlos and England international Ollie Watkins sealed a third victory in four Group E matches for the Villans.
The Premier League side remain in second place in the section following Legia Warsaw's win over Zrinjski Mostar earlier in the day, however Villa now possess a six-point buffer over the third-placed Bosnians with only two games left to play.
Villa made four changes to the XI which produced a limp display in the defeat at Nottingham Forest on Sunday, with Brazilian Carlos, Clement Lenglet, Youri Tielemans and Leon Bailey coming into the hosts' starting lineup as they looked to complete the double for their Dutch counterparts.
With youngster Ruben van Bommel and Ibrahim Sadiq boasting just one Eredivisie goals between them, AZ's offensive threat arrived in the form of striker Pavlidis, who was expectedly named at the focal point of the visitors' attack after finding the net against NEC last time out.
After dismantling Alkmaar on their own patch during their last European adventure, it was no surprise that Villa started the game brightly in front of an expectant crowd in the Second City, and Unai Emery's men had the ball in the back of their opponents net in the opening three minutes.
The returning Bailey picked up the ball on the right flank following Watkins' strike firing off the post, and the Jamaican provided a cross for former Barcelona man Lenglet who headed in, however the winger was offside after taking the original corner.
There was little goalmouth action in the first period but the Dutch visitors did grow into the contest as the half-time break approached, and a free-flowing move from Pascal Jansen's men was finished off by leading marksman Pavlidis, however midfielder Sven Mijnans was offside in the build-up.
Despite Villa's dominance possession wise, AZ were starting to realise the frailties surrounding the hosts' high line, and shortly after the break the Eredivisie title chasers took the lead courtesy of their most-potent attacker in the opening months of the 2023-24 term.
Centre-back Riechedly Bazoer spotted the run of Greek international Pavlidis off the back of Lenglet, and the Dutchman produced a long ball for the 24-year-old striker, who evaded the attentions of the Emery's backline before dinking the ball over the onrushing Emiliano Martinez to put the visitors ahead.
The Villans responded well to going behind in the contest and could have been level when Lucas Digne's cross found the run of Boubacar Kamara, however the French youngster's effort on goal ballooned above the crossbar and left the Villa Park crowd wondering whether it would be their side's night.
With referee Luis Miguel Branco Godinho wrongly judging that Jordy Clasie had managed to get a decisive touch on Kamara's shot, Villa were awarded a corner which led to their equaliser, with Bailey finding the head of Carlos, who netted his first-ever strike in European competition.
Although AZ posed a threat on the break with the arrivals of Ernest Poku and Myron van Brederode from the bench, Emery's men were in the ascendency following their goal, and it did not take long for the Premier League outfit to take complete control of the contest for the first time.
Substitute Douglas Luiz picked up the ball as Alkmaar were camped around their penalty area, and the Brazil international delivered a perfectly-weighted ball over the visitors' backline into the path of Watkins, who guided the ball into the near post with a header past the helpless Matthew Ryan.
Villa had chances to extend their advantage in the closing stages but did well to see out their success, with the Second City club welcoming Marco Silva's Fulham to Villa Park on Sunday afternoon, aiming to avoid back-to-back domestic defeats for the first time this term.
With AZ's progression in the Conference League in serious jeopardy following defeat in England, Jansen's men will turn their attentions to Eredivisie matters on Sunday when they travel to Dutch champions Feyenoord, with Alkmaar currently level on points with Arne Slot's charges.