Использовать маску со значениями True / False
# All pixels should be normalized 0..1 or 0..254
first_img = np.random.rand(1920,1080,3)
second_img = np.random.rand(1920,1080,3)
eps = 0.01 # Black pixel threshold
mask = first_img.sum(axis=2) > eps
for i in range(first_img.shape[2]):
first_img[:,:,i] = (first_img[:, :, i] * mask) + ((1 - mask) * second_img[:, :, i])