First, to see the impedance, go to "Results->S parameter Calculations->Calculate Z and Y matrixes", then go to 1D results tree, choose Z Matrix. Then you can see the Real, Image, Mag and phase of the impedance in the whole frequency range. It is calculated from the S parameters, so it is actually the impedance that you SEE from the port.
So, this is the impedance that you see from the port, including all the components, it's simply something like a Thevenin equivalence of the whole structure.
The impedance of the patch antenna depends on where you excite it. You know that this is a resonant structure with a dominant mode. In that mode, there is a certain arrangement of E and H fields. So, in different points of the patch you see different impedances, and that the way to match the antenna to feeds with different impedances. For example, if you have a prob-fed patch, you can move the location of the probe, and if you have a microstrip-fed patch, you make notches.
I coudln't be sure how did you feed the patch, if it is by a microstrip and if the microstrip line is a 50 Ohm, you can simply assume that the port is at the end of the feedline, which means what you calculated is more or less the impedance of the antenna. To be nore precise (mostly for phase), you can change the reference plane in port definition, and put it next to the antenna.
If you also put your cst file (a zipped project including the file and the associated directory), we can be more helpful.
Matt