Heat oil in heavy medium skillet over medium-high heat. Add eggplant and onion and sauté until vegetables soften and brown lightly, about 10 minutes. Season with salt and pepper.
Unroll pizza dough. Fit into prepared pan, pressing up at edges to create 1-inch-high rim. Spread eggplant mixture evenly over bottom of crust. Arrange tomatoes over. Sprinkle with cheese and marjoram. Bake until topping is heated through and edges of pizza are brown and crisp, about 15 minutes. Cut into squares.