We examine the time-dependent distortion of a nearly circular viscous domain in an infinite viscous sheet when suction occurs. Suction, the driving force of the instability, can occur everywhere in the two phases separated by an interface. The model assumes a two-dimensional Stokes flow; the selection of the wavelength at short times is determined by a variational procedure. Contrary to the viscous fingering instability, undulations of the boundary may be observed for enough pumping, whatever the sign of the viscosity contrast between the two fluids involved. We apply our model to the suction by lipoproteins of cholesterol-enriched domains in giant unilamellar vesicles. Comparison of the number of undulations given by the model and by the experiments gives reasonable values of physical quantities such as the viscosities of the domains.