In a medium bowl, whisk together the soy sauce, rice vinegar, honey, sesame oil, cornstarch, minced garlic, grated ginger, and black pepper until smooth. Place the thinly sliced beef in a separate bowl and pour half of the sauce mixture over it. Toss to coat thoroughly and let marinate for at least 10 minutes while you prep the vegetables. Reserve the remaining sauce.
Heat 1 tablespoon of vegetable oil in a large skillet or wok over medium-high heat. Add the sliced onion and bell peppers. Stir-fry for 5-7 minutes, until the vegetables are tender-crisp and have some charred spots. Remove the vegetables from the skillet and set aside on a plate.
Add the remaining 1 tablespoon of oil to the hot skillet. Add the marinated beef in a single layer, letting it sear undisturbed for 1 minute. Then, stir-fry for 2-3 more minutes until the beef is just cooked through and browned.
Return the cooked vegetables to the skillet with the beef. Pour in the reserved sauce. Stir everything together and bring to a simmer. Cook for 1-2 minutes, stirring constantly, until the sauce has thickened and coats the beef and vegetables evenly.
Divide the hot cooked rice among four bowls. Spoon the beef and pepper stir-fry over the rice. Garnish with sliced green onions and sesame seeds. Serve immediately.