Preheat oven to 350° F. Line a 12-count muffin tin with paper liners or spray with non-stick spray. Set aside.
In a large bowl, whisk together the flour, cocoa powder, baking soda, baking powder, salt, and sugar. Set aside.
In a separate bowl or measuring cup, whisk together the buttermilk, oil, egg, egg yolk, vinegar, and vanilla.
Pour the wet ingredients into the dry, mixing just until there are no streaks of flour left. Be careful not to overmix.
Scoop batter into cupcake liners, filling about halfway full. Bake for 17-19 minutes, or until a toothpick comes out clean. Remove from the oven and place on a wire cooling rack for 5 minutes, and then remove from the pan to cool completely.