In my Mathematics program in the US, you could (with a Bachelor's) apply either to the Master's program or the PhD program directly. You could also (I think, though it's not what I did so I'm not sure) move from the Master's program to the PhD without reapplying, or get your Master's from the PhD program as an intermediate step.
However, while all of these were options, you were best off applying directly to the PhD program no matter what your intentions were. You were more likely to be offered funding if you were pursuing a PhD.