Preheat the oven to 350°F and line an 8x8-inch pan with parchment paper so the bars lift out easily after baking.
Melt the butter in a medium saucepan over low heat. Remove from heat and stir in the sugar until combined.
Add the eggs one at a time, stirring well after each addition. Mix in the cocoa powder, flour, and salt until no dry streaks remain.
Fold in the chocolate chips. Spread half the batter into the prepared pan.
Drizzle the caramel sauce evenly over the first layer of batter. Spread the remaining batter on top to cover the caramel.
Bake for 25 to 28 minutes until the center is set. Remove from the oven and immediately sprinkle the flaky sea salt over the top.
Let the bars cool completely in the pan before lifting them out and cutting into four large squares.