It's important to be specific about what you mean by "masters programme" as you could get different answers based on different expectations of what you mean.
If by this you mean an integrated undergraduate masters MPharm, then you could still apply, but you would still need to meet the academic requirements. Doing the apprenticeship will not change that, and so if you didn't meet the requirements before and haven't resat any of your A-level exams in order to get the required grades to meet those, you won't be accepted.
If however by "masters" you mean a postgraduate qualification (e.g. MSc, MRes, MPhil etc) which would usually not be a qualifying degree to enter that profession but more typically a research or advanced practice type degree, I expect you will need some kind of undergraduate degree first and a 2 year apprenticeship is unlikely to meet those requirements.
In either event an apprenticeship isn't going to ordinarily allow you to bypass academic requirements for a degree, and unless that apprenticeship has an academic qualification attached that meets the requirements (e.g. a degree apprenticeship which may be acceptable for some postgraduate masters degrees) it's really neither here nor there.