Combine the squid, vinegar, and water in a small pot over medium heat; season with salt and pepper. Cook for 10 minutes.
Meanwhile, heat the olive oil in a saucepan over medium heat; cook and stir the onion and garlic in the hot oil until softened, 5 to 7 minutes. Stir the tomato and soy sauce into the mixture. Pour the squid mixture into the saucepan and bring to a simmer; cook together another 20 minutes.
