Synchrotron radiation of ultra-relativistic particles accelerated in a pulsar wind nebula may dominate its spectrum up to gamma-ray energies. Because of the short cooling time of the gamma-ray emitting electrons, the gamma-ray emission zone is in the immediate vicinity of the acceleration site. The particle acceleration likely occurs at the termination shock of the relativistic striped wind, where multiple forced magnetic field reconnections provide strong magnetic fluctuations facilitating Fermi acceleration processes. The acceleration mechanisms imply the presence of stochastic magnetic fields in the particle acceleration region, which cause stochastic variability of the synchrotron emission. This variability is particularly strong in the steep gamma-ray tail of the spectrum, where modest fluctuations of the magnetic field lead to strong flares of spectral flux. In particular, stochastic variations of magnetic field, which may lead to quasi-cyclic gamma-ray flares, can be produced by the relativistic cyclotron ion instability at the termination shock. Our model calculations of the spectral and temporal evolution of synchrotron emission in the spectral cut-off regime demonstrate that the intermittent magnetic field concentrations dominate the gamma-ray emission from highest energy electrons and provide fast, strong variability even for a quasi-steady distribution of radiating particles. The simulated light curves and spectra can explain the very strong gamma-ray flares observed in the Crab nebula and the lack of strong variations at other wavelengths. The model predicts high polarization in the flare phase, which can be tested with future polarimetry observations.