Heat oven to 400°. Spray 2 cookie sheets with cooking spray. Unfold pastry on lightly floured surface. Roll into 12-inch square, trimming edges to make even. Cut into 6 rows by 6 rows to make 36 (2-inch) squares. Place on cookie sheets. Bake 12 to 15 minutes, rearranging cookie sheets after 6 minutes, until puffed and golden brown. Remove from cookie sheets to wire rack. Cool until slightly warm.
Meanwhile, melt butter in 8-inch skillet over medium heat. Cook onion in butter 15 to 20 minutes, stirring occasionally, until tender. Stir in brown sugar. Cook and stir until onions are coated. Stir in tomatoes. Remove from heat; keep warm.
Place cooled pastry squares on same cookie sheets. Press cheese piece into center of each pastry square. Fill with about 1 teaspoon onion mixture. Bake about 1 minute or until cheese is melted.