Preheat oven and bake pastry shells according to package directions and set aside.
Meanwhile, in a large skillet over medium-high heat, melt the butter or margarine. Add the onions and garlic and cook until the onions are tender, about 5 minutes.
Add flour, stirring to coat the onions and garlic.
Add the milk, tomatoes, salt, and pepper. Bring to a boil, stirring constantly until thickened; then reduce heat to low.
Add the chicken and cook for 2 minutes until heated through.
Spoon chicken mixture into warm pastry shells.