Obstruction/Interference/Nothing

[THREE]

Runner from third goes home. A play is made on the runner at home base. As this is happening, the runner from second advances to third--third baseman is standing in the middle/on top of third base. The runner who is advancing from second to third "intentionally" runs into the fielder who is standing on the base. Even though the contact was intentional, I did not judge it to be violent or malicious. I know this is a fine line-but that was my decision/judgement. After the runner intentionally runs into the fielder standing on top of the base, the play at home is completed with runner being out and catcher maintains control of the ball. After the collision between runner/3rd baseman everything stops at 3rd also. What (if anything) should be done concerning intentional contact? There is no question that is was intentional. Is was if "Hey-this is a warning-stay out of the way" type hit.