Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic [1,2]. However, the emergence of vaccine-resistant strains [3-6] may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic [7,8]. To quantify and characterize the risk of such a scenario, we created a SIR-derived model [9,10] with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. We found a counterintuitive result that the highest probability for the establishment of the resistant strain comes at a time of reduced non-pharmaceutical intervention measures when most individuals of the population have been vaccinated. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions [7,11,12] throughout the entire vaccination period.