Put an oven rack in the lower third of the oven and preheat it to 325F. Line an 8-inch square baking pan with parchment paper.
Make a double boiler, which is a saucepan filled with about 2 inches of simmering water with a bowl on top. The steam from the water heats up the bowl to seamlessly melt all the ingredients together. In the bowl, combine butter, sugar, cocoa powder, and salt. Ensure the simmering water isn't touching the bottom of the bowl. Stir until the mixture is incorporated and warm. The mixture will appear quite gritty but become smooth once all ingredients are added.
Remove the bowl from the heat and set aside to cool for about 5 minutes, until no longer hot. Stir in the vanilla. Then whisk in 1 egg at a time. Stir vigorously to incorporate. The batter should now look shiny and thick.
Stir in the flour. Beat vigorously until everything is thoroughly incorporated.
Spread evenly in the lined pan and bake for 20 minutes.
While the brownies bake, prepare the pecan pie topping. In a medium bowl, combine sugar, flour, egg, vanilla, salt, and melted butter. Fold in the chopped pecans.
Remove the partially cooked brownies from the oven and pour the pecan pie mixture evenly on top. Gently press the full pecans on top of the pecan pie mixture.
Return to the oven to bake for an additional 20-25 minutes, turning halfway. These brownies are very fudgy in texture and you can tell they are done by inserting a toothpick and it coming out clean.
Let cool for 5-10 minutes before cutting. Serve warm!