In a small saucepan, bring the tomato-basil sauce and red pepper flakes to a simmer over medium heat. Cook uncovered until thick, 20 to 25 minutes. Remove the pan from the heat and stir in the basil.
Preheat the broiler.
Place six 5-ounce ramekins on a baking sheet. Divide the sauce equally among the ramekins. Divide the prosciutto among the ramekins. Place the slices of mozzarella between 3 paper towels to absorb any excess moisture. Place the slices of mozzarella on top of the prosciutto. Season with salt and pepper. Sprinkle the Gruyere on top.
Broil until the cheese is melted and golden brown, 5 to 8 minutes. Serve with grilled bread.