Preheat the oven to 350 degrees F. Line a 9-inch-square baking dish with foil, leaving a 2-inch overhang on two sides; coat the foil with cooking spray. Pulse 2 cups flour, the butter, confectioners' sugar, 1 teaspoon vanilla and the salt in a food processor until the mixture starts clumping together, about 1 minute. Press firmly and evenly in the bottom and 1/4 inch up the sides of the prepared pan. Bake until firm and lightly browned, 25 to 30 minutes. Transfer to a rack and let cool 5 minutes.
Meanwhile, combine the dulce de leche, heavy cream, egg yolks and the remaining 1 tablespoon flour and 2 teaspoons vanilla in a medium bowl and whisk until smooth. Pour the mixture over the crust and sprinkle with the chocolate chips and pecans. Return to the oven and bake until set around the edge but slightly jiggly in the center, 20 to 25 minutes.
Transfer to the rack and let cool completely. Lift out of the pan using the overhanging foil. Remove the foil and cut into pieces.