Position rack in middle of oven. Preheat oven to 325 degrees F. Coat a 9-inch square pan with nonstick spray.
Melt the chocolate and butter together in the microwave or in top of double boiler; whisk until smooth and cool slightly.
Whisk in sugar and brown sugar until combined. Whisk in vanilla then eggs, one at a time, allowing each one to be absorbed before adding the next.
Switch to a large rubber spatula and fold in flour, salt pomegranate seeds and cacao nibs just until mixture is combined. Scrape into prepared pan.
Bake for about 30 to 35 minutes or until slightly puffed and the edges have just begun to come away from the sides of the pan. A toothpick inserted in the center will come out with a few moist crumbs clinging. Do not over-bake. Cool completely in the pan set on a rack. Cut into 25 (5x5) bars. Store at room temperature for up to 2 days in an airtight container in single layers separated by parchment paper.