Preheat oven to 350 degrees F. Line a 9 inch square pan with foil, draping foil over edges. Spray foil with nonstick spray.
In a large saucepan, melt butter with chocolate over low heat, stirring occasionally. When mixture is melted and smooth, remove from heat. Whisk in cocoa, then sugar, then eggs, then vanilla and then flour, making sure that each is incorporated before adding the next. Pour batter into prepared pan. Sprinkle flaky sea salt over the top of the batter.
Bake brownies for about 35 minutes, until edges are set but the center is still a bit soft. A toothpick inserted into the center should come out coated with a little bit of the batter. You want them to remain fudgy and not come out dry.
Let brownies cool at room temperature for about an hour, then refrigerate just until firm (about another hour). At this point, gently lift brownies from the pan and peel back the foil. Cut brownies into squares and serve.