The smallest 9mm Semi-auto pistols are:
Diamondback DB9
Boberg XR9-S
Rohrbaugh R9S
These are the absolute smallest 9mm semi-autos that I'm aware of. The Rohrbaugh is a good gun, but not meant to be a range toy, not rated for +p and you will need to have spare recoil springs.
The Diamondback DB9 is inexpensive, doesn't like +P, and prefers ball ammo over hollow points. Some say they have had problems with theirs; mine works fine with the right ammo.
The Boberg XR9S is a well made gun, handles +P and hollow points, but doesn't like certain ammo that is not crimped - Boberg/Bond Arms has a big list of ammo that will work and a short list of ammo that will not work. With the right ammo, it is very reliable.
The Kimber Micro 9 is a tad bigger than the 3 listed above. I don't include it because it is not "the smallest".