Diphenyl guanidine (DPG) is the most commonly used secondary accelerator in silica-reinforced rubber compounds because of its additional positive effect on the silanization reaction and deactivation of free silanol groups that are left over after the silanization. However, because of health and safety concerns about the use of DPG, which decomposes to give highly toxic aniline during high processing temperature, safe alternatives are required. This work investigates the effect of various types of aliphatic amines having alkyl or cyclic structures and similar pKa (i.e., hexylamine [HEX], decylamine [DEC], octadecylamine [OCT], cyclohexylamine [CYC], dicyclohexylamine [DIC], and quinuclidine [QUI]) on the properties of silica-reinforced natural rubber (NR) compounds by taking the ones with DPG and without amine as references. When compared with the compound without amine, the use of all amine types reduces filler–filler interaction (i.e., the Payne effect) and enhances filler–rubber interaction, as indicated by bound rubber content and decreased heat capacity increment. The amines with alkyl chains can reduce the Payne effect and enhance cure rate to a greater extent compared with the amines with cyclic rings as a result of better accessibility toward the silica surface and a shielding effect because of less steric hindrance. The longer carbon tails on linear aliphatic amines ranging from HEX, DEC, to OCT lead to a lower Payne effect, lower heat capacity increment, higher bound rubber content, and higher modulus as well as tensile strength. Overall, the use of OCT provides silica-reinforced NR compounds with properties closest to the reference one with DPG and can act as a potential alternative for DPG.