Bolted flange joints in fuzes undergo high acceleration during penetration, along with nonlinear responses which are forced reaction, structural vibrations, and shock effects. Vibrations of high frequencies aggregate noises and make it harder for the signal processing of fuzes. This study proposed an effective and innovative method of suppressing vibrations of high frequencies caused by impact loading. Shear thickening fluids (STFs) were stuffed into bolted flange joints. A damper of 57 vol/vol% dense silica particle-ethylene glycol suspension was inserted into gaps between the surfaces of the incident bar and the flange. Based on a modified split Hopkinson pressure bar, pulse widths, amplitudes, and structural frequencies of both impact and vibrational response regions were evaluated to examine the effectiveness of the STF damper. The amplitude and pulse width in the vibrational response region were significantly reduced, since this suspension forms jamming clusters subjected to impulses, attenuating the shockwaves. The STF fillers under various lengths of projectiles from 50 mm-400 mm were discussed to validate effectiveness. Further comparisons with epoxy resin fillers with various curing times indicated that the STF inhibited high frequency oscillations as a protector, and damped the dominant frequency of the original structure. However, experimental data showed that the transmission pulse of the incident bar was similar to joints without protection, indicating that the force transmission ratio was not affected by the fillers. These results show the feasibility of STFs as energy absorbers for vibration reduction of bolted flange joints.