Despite their prominence in "Italian" style cuisine, tomatoes were not native to Europe until they were brought over from the New World in 1522. At first they were believed to be poisonous, but the lower-classes began to incorporate them into their cuisine over the next several years.
The first pizza which used tomatoes, originated in Naples. Tomatoes were chopped and added directly into the yeast dough.
Sauce it the most common use for tomatoes in pizza, in most worldwide pizzerias it's seasoned with olive oil and Italian herbs, but in most traditional pizzas they can be a sole-ingredient sauce with not even salt added, though in some Italian pizzerias it could include carrot puree added to lower the acidity that chopping the seeds can cause.
Some counted pizzas include sliced tomatoes as a topping, specially the Margarita swhich includes tomato slices through the pizza surface but it can also be cut on cubes depending on the restaurant style.