Preheat the oven to 400 degrees F.
Heat the olive oil in a small saucepot over medium-low heat. Add the onions and saute until translucent, 2 to 3 minutes. Add in the garlic and saute for 1 minute. Add in the tomato paste and saute for 1 more minute. Stir in the diced tomatoes, sugar and season with salt and pepper. Add the torn basil leaves and bring to a slow simmer. Allow to simmer for about 15 minutes while you make your pizza pocket.
Roll out the dough balls on a lightly floured surface into 4 equal rounds. On half of each round, layer some mozzarella, and then some pepperoni slices. Fold in half, covering the filling, and then fold the outer edges up and crimp the edges with your fingers to seal. Place the pockets on a baking sheet, brush with olive oil and sprinkle with grated Parmesan. Bake until golden, 10 to 15 minutes. Serve with the sauce on the side.