The acoustic nonlinearity parameter is determined from the amplitudes of the fundamental and second harmonic component of the acoustic wave propagating through the material. However, the generally used through-transmission based measurements with PZT transducers contain high system nonlinearity, so that the received second harmonic component includes an extra component caused by the transducer, which significantly decrease the reliability of measurements. In this study, we proposed a novel method to reduce the system nonlinearity in the conventional through-transmission based measurements by adding a simple process in which the transmitting and receiving transducers are in direct contact without a specimen. The proposed method was experimentally validated for two materials, Al6061-T6 and Fused Silica. For both materials, several specimens with different thickness were prepared, and the measurement results showed that the magnitude of the second harmonic was proportional to the thickness, but there was an offset due to system nonlinearity. On the other hand, after applying the proposed technique, the offsets were greatly reduced, and furthermore, this performance was maintained even when the transducer setup was changed, and the ratio of nonlinearity parameters measured for the two materials was in good agreement with the known literature value.