Preheat oven to 350ºF; line 2 baking sheets with baking paper, lightly coated with cooking spray. I used Silpats! Lightly spoon flour into a dry measuring cup; level with a knife. Sift together flour, soda, and salt; set aside.
Melt butter in a large saucepan over medium heat. Remove from heat; stir in cocoa powder and sugars (mixture will resemble coarse sand). Add yogurt and vanilla, stirring to combine. Add flour mixture, stirring until moist. Wrap the chocolate dough around the caramel balls. Place balls on cookie sheets and sprinkle with sea salt.
Bake for 10-12 minutes or until almost set. Cool on pans 2 to 3 minutes or until firm. Remove cookies from pans; cool on wire racks.