Super-imposed synchronization sequences for the data-aided time and frequency offset estimation, compared to appended synchronization sequences, can reduce the training overhead and peak-to-average power ratio (PAPR) of the transmitted signal in orthogonal frequency division multiplexing (OFDM) based communication systems. However, synchronization sequences with good correlation properties have a wide frequency spectrum and their separation from the useful signal poses a serious problem, especially if the communication channel is time dispersive. This paper describes a novel method that allows to remove a super-imposed synchronization sequence of unknown magnitude from an equalized OFDM signal by means of frequency-domain matched filter. The problem of the super-imposed synchronization sequence impact on the pilot symbol assisted channel estimation is discussed. Efficiency of the synchronization sequence suppression along with bit error ratios of communication systems with several popular synchronization sequences and pilot tone patterns are evaluated using numerous computer simulations.