Pat the beef short ribs dry with a paper towel and season all sides evenly with sea salt and black pepper.
Heat the ghee in a small Dutch oven or heavy-bottomed pot over medium-high heat until shimmering.
Place the short ribs in the pot and sear for 2-3 minutes per side until a deep golden-brown crust has formed, then remove the meat and set it aside on a plate.
Reduce the heat to medium and add the diced onion, chopped carrots, and chopped parsnips to the same pot, sautéing for 5 minutes until the onions are translucent.
Add the minced garlic and cook for 60 seconds until fragrant, being careful not to let it burn.
Pour in the balsamic vinegar to deglaze the pot, using a wooden spoon to scrape up all the flavorful browned bits from the bottom.
Return the beef short ribs to the pot and pour in the beef bone broth until the meat is roughly half-submerged.
Tuck the rosemary and thyme sprigs into the liquid, bring to a gentle simmer, then cover with a tight-fitting lid.
Lower the heat to the lowest setting and braise for 2.5 to 3 hours, or until the beef is tender enough to pull apart with a fork.
Discard the herb sprigs and serve the beef alongside the braised root vegetables with a drizzle of the remaining cooking liquid.