In extremely low-light conditions, random telegraph signal (RTS) noise and dark current white defects become visible. In this paper, a multi-aperture imaging system and selective averaging method which removes the RTS noise and the dark current white defects by minimizing the synthetic sensor noise at every pixel is proposed. In the multi-aperture imaging system, a very small synthetic F-number which is much smaller than 1.0 is achieved by increasing optical gain with multiple lenses. It is verified by simulation that the effective noise normalized by optical gain in the peak of noise histogram is reduced from 1.38e⁻ to 0.48 e⁻ in a 3 × 3-aperture system using low-noise CMOS image sensors based on folding-integration and cyclic column ADCs. In the experiment, a prototype 3 × 3-aperture camera, where each aperture has 200 × 200 pixels and an imaging lens with a focal length of 3.0 mm and F-number of 3.0, is developed. Under a low-light condition, in which the maximum average signal is 11e⁻ per aperture, the RTS and dark current white defects are removed and the peak signal-to-noise ratio (PSNR) of the image is increased by 6.3 dB.