Is providing more references than the required number in my PhD application acceptable?
It's usually best to carefully read the application's supporting materials (FAQ, 'help' section, explanation pages, etc.), as some programs I've seen explicitly say "please do not send more than 2 [or usually 3 in the US]". Some programs require 2, but allow 3 (I've seen fellowships accept up to 5, but not a PhD program that does that).

However, I mainly answered to suggest you carefully consider how you pick your two "guaranteed" reference letters. If you are going into a program that is friendly towards industry practitioners, and your job and experience is relevant, and if your industry writer would be in a position to talk about relevant aspects of your application (technical skills desirable to the program, work ethic, reliability, etc), then it is possible that such a letter is actually better than a bland academic one by itself. This varies heavily by field, but if the program explicitly says something about how to professional references are OK (often with a stipulation that at least 1 be from an academic), then I think there's a case for you to go with one academic and one professional letter. Then you can put the 3rd in, if the system allows it, as your additional academic reference.

This can be very field and program specific, so I'd advise you to try to get some more guidance from someone closer your target program to give you there advice. But some fields - especially in applied areas of computer science, like many robotics programs, software engineering, etc - are far more appreciative of certain kind of professional reference letters than others.