A novel and simple method for the preparation of silica nanoparticles having surface-functionalized diamino moiety (dASNPs) was reported in our paper and characterized using scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectrometry, and thermogravimetry techniques. To test this method practically, in this contribution we describe the enhanced separation of four plant auxins indole-3-acetic acid (IAA), indole-3-butyric acid (IBA), 2,4-dichlorophenoxyacetic acid (dCPAA), and 2-(1-naphthyl) acetic acid (NAA) by capillary electrochromatography using diamino moiety functionalized silica nanoparticles as pseudostationary phase (PSP) in the running buffer. The effect of pH, buffer concentration, and diamino moiety functionalized silica nanoparticles concentration on the selectivity of separation was investigated. A combination of the nanoparticles and running buffer reversed the electroosmotic direction making possible the rapid and efficient separation of the auxins from the auxins migrated in the same direction with the EOF under optimum experimental conditions. A good resolution of four auxins was obtained within 5.5 min under optimum experimental conditions. The precision (RSD, n = 5) was in the range of 0.720.91% and 1.892.23% for migration time and peak area response, respectively. The detection limits were 0.48, 0.44, 0.46, and 0.42 mu M for NAA, IBA, IAA, and dCPAA, respectively. Furthermore, the method was successfully tested for the determination of IAA in the grapes.