Combine cake mix, water, and eggs in a bowl, and beat at medium speed of a mixer 2 minutes.
Divide batter evenly among 24 muffin cups coated with cooking spray. Bake at 350° for 20 minutes or until a wooden pick inserted in center comes out clean. Cool 10 minutes; remove from pans, and cool on a wire rack.
Split each cupcake in half horizontally using string or a serrated knife.
Combine chocolate chips, milk, and cocoa in the top of a double boiler. Cook over simmering water until chocolate melts, stirring occasionally. Remove from heat; stir in 2 cups powdered sugar and vanilla. Spread 2 teaspoons chocolate mixture over bottom half of each cupcake; top with top halves. Sift 2 tablespoons powdered sugar over tops of cupcakes.