What I understand from your question is:
Using export option in HFSS, you are getting Freq in GHz and S11 in magnitude.
And from your network analyzer you are getting Freq and S11 (real) and S11 (imaginary), Is that right?
If I am correct, then do the following:
Since you are getting real and imaginary from the VNA, take the magnitude of the values. i.e sqrt(realvalue^2 + imagvalue^2).
The value should be more or less the same as that you got from HFSS.
For plotting in Matlab, export the excel sheet which has freq and the corresponding values of S11 in matlab and you can plot them.
If you are still having problems, upload the excel sheet. I think I can help you out.