Some embodiments of the present invention provide a system that accurately synchronizes signals related to the operation of a computer system. During operation, the system receives a first time-domain signal associated with a first system variable and a second time-domain signal associated with a second system variable from the computer system. The system then transforms the first and the second time-domain signals into a first frequency-domain signal and a second frequency-domain signal, respectively. Next, the system computes a cross-power-spectral-density (CPSD) between the first and second frequency-domain signals to obtain a phase angle versus frequency graph between the two frequency-domain signals. The system subsequently extracts the slope of the phase angle versus frequency graph, and uses the value of the slope to synchronize the first time-domain signal and the second time-domain signal.