If they really are tiny pebbles, shampooing the carpet won't remove them. What you need is something to lift them up so the vacuum cleaner can grab them.

One suggestion is to blow them with compressed air. You will need a very fine nozzle on your compressed air line to do this. Another possibility is to use a very stiff bristle brush to get down to where they are in the carpet and get them moving around. As you are doing this, use the fine orifice vacuum wand with your other hand to suck them up once you dislodge them.