pH describes the [H+] in a solution on a log scale that is easier to think about than the actual concentrations in molarity. The lower the pH, the more concentrated the H+ in solution.
pKa describes the acidity of a compound. It can be thought of as a physical property, describing the strength of an acid.
You question is analogous to asking what the difference is between temperature and boiling point. One describes the heat in the environment (and thus varies) while the other describes the compound and the state it's in at a given temperature. Raising the temperature does not change the boiling point, but can convert the compound into a gas.
Lowering the pH does not change the pKa for the acid, but it does change the amount that is in the protonated state.
Hope this helps.