Phase separation in fuel you pulled from your tank will only occur if the fuel contained more water than the chemical saturation limit. That water can be in the fuel in the form of emulsified water and finely dispersed tiny water droplets. Once the fuel sits for a while, dispersed water droplets and later emulsified water will separate from the fuel and form a distinct water layer. However, if the fuel was merely water saturated, phase separation will not occur unless you lower the temperature of the fuel to generate super saturation. Furthermore, putting the fuel in an open container will allow water to evaporate from the fuel if the saturation level of the air the fuel is exposed to is less than the saturation level of the fuel. That will decrease the water content of the fuel. That said, your fuel certainly has water in it, likely on the order of 50-100 ppm water. The chemical solubility of diesel fuel is not a single number because diesel fuel does not have a constant composition.

Getting the water out of the fuel is rather difficult. Vacuum flashing the fuel will also deplete the fuel in low molecular weight components. As Rich said, exposing the fuel to a water sorbent medium will be more effective. However, short of exposing the fuel to a perfectly dry gas for a very long time, getting all the water out is basically impossible