Shalom dear Rabbi,
Question: I got a loaf of bread and made a pizza, put cheese and tomato on top, which brachar should I make Chamotzi?
Yes, the bracha is still hamotzei, because it is still halachically considered bread. If the pieces would be smaller than a k’zayis and the pieces would be cooked in a pot of water then it would change the bracha, however from what you are describing the bracha will remain the same.
Shulchan Aruch O:CH 168-10,12.