The striker celebrated his England call-up to nod in with nine minutes left for a 2-1 win and put Villa on the brink of the Europa Conference League knockout stages.
Diego Carlos’ controversial goal – heading in a corner which should have never been given – quickly cancelled out Vangelis Pavlidis’ opener.
Victory left Villa joint-top of Group E, behind Legia Warsaw on their head-to-head record, knowing a point from their final two games would guarantee progress.
Legia’s 2-0 win over Zrinjski Mostar earlier on Thursday had put the Polish side three points clear in the group.
Villa knew victory would virtually secure second spot and their superiority was telling early, the hosts thinking they had the lead after just three minutes.
Ezri Konsa’s shot was deflected behind and, from the corner, Watkins header was cleared off the line by Pavlidis. The ball ran to Leon Bailey and his cross was nodded in by Clement Lenglet – only for VAR to rule the goal out with Bailey offside.
Mat Ryan tipped Youri Tielemans’ shot behind as Villa looked to regain some momentum but there would have been frustration for Emery as their early edge slipped away.
Alkmaar even had their own goal disallowed three minutes before the break when a neat move ended with Pavlidis tapping in, although the striker was comfortably offside.
The striker then tested Martinez after Villa played themselves into trouble as the visitors ended the half on top.
It proved a warning sign as, six minutes into the second half, the striker opened the scoring with a goal of pure simplicity.
Villa were caught out by Riechedly Bazoer’s ball over the top as Pavlidis ran clear of Lengent and beat Martinez for his 15th goal of the season.
Alkmaar had something to cling to, having been 3-0 down at the same stage in the Netherlands two weeks ago, and Yuki Sugawara’s shot deflected wide.
Somewhat inevitably, when Bailey delivered the ball Diego Carlos nodded in.
It gave Villa renewed confidence and, with time running out, Watkins grabbed the winner when he stole in ahead of Jordy Clasie to nod in Douglas Luiz’s fine pass.