We study the phase fluctuations in the normal state of a general two-dimensional (2d) superconducting system with s-wave pairing. The effect of phase fluctuations of the pairing fields can be dealt with perturbatively using disorder averaging, after we treat the local superconducting order parameter as a static disordered background. It is then confirmed that the phase fluctuations above the 2d Berenzinskii-Kosterlitz-Thouless (BKT) transition give birth to the pseudogap phenomenon, leading to a significant broadening of the single-particle spectral functions. Quantitatively, the broadening of the spectral weights at the BCS gap is characterized by the ratio of the superconducting coherence length and the spatial correlation length of the superconducting pairing order parameter. Our results are tested on the attractive-U fermion Hubbard model on the square lattice, using unbiased determinant quantum Monte Carlo method and stochastic analytic continuation. We also apply our method to 2d superconductors with d-wave pairing and observe that the phase fluctuations may lead to Fermi-arc phenomenon above the BKT transition.