Phase measurements are made using S-parameters, just like amplitude measurements. A phase measurement is a relative (ratio) measurement and not an absolute measurement. Phase measurements compare the phase of the signal going into a device (the incident signal) to the phase of the device's response signal. The response signal can be either reflected or transmitted. Assuming an accurate calibration has been performed, the difference in phase between the two signals (known as phase shift) is a result of the electrical characteristics of the device under test.
The following graphic shows the phase shift (in time or degrees) between an incident signal and a transmitted signal (as might be seen on an oscilloscope display).