Preheat oven to 375°. Cut eggplant into 1" cubes and toss with kosher salt, let sit 10-15 minutes. Cut zucchini and yellow squash into 1" thick rounds or half moons and put into large mixing bowl. Cut onion into large dice and add to mixing bowl.
Heat skillet over medium high heat and add 1 tbsp olive oil. Saute garlic and Italian seasoning stirring frequently for 1 minute to brown garlic. Add tomatoes and pepper, stir well.
Pat eggplant dry with paper towels and add to mixing bowl along with tomato mixture, stir to combine. If vegetable mixture seems too dry add a little of the reserved juice from the canned tomatoes.
Pour vegetable mixture into oiled 9x13 glass baking dish and bake for 45-50 minutes stirring once halfway through baking time. Vegetables should be tender and browning on top. Top with fresh basil and serve.