Pat the beef dry and season it with the salt and pepper. Heat 1 tablespoon oil in a Dutch oven and brown the beef in batches; transfer to a plate.
Heat the remaining oil in a skillet and brown the pearl onions for 8 to 10 minutes. Set aside.
Braise the Stifado:
Add the garlic and tomato paste to the Dutch oven and cook for 1 minute. Pour in the wine and scrape up the browned bits.
Return the beef and add the tomatoes, stock, vinegar, cinnamon, allspice, bay leaves, and oregano. Bring to a simmer, cover, and cook on low for 90 minutes.
Add the browned onions and continue simmering partly covered for 45 to 60 minutes, until the beef is tender and the sauce is thick. Remove the whole spices before serving.
Notes
Keep the braise at a gentle simmer; rapid boiling can toughen the beef.