Preheat oven to 350°F. Partially peel eggplants in 1-inch strips, using a vegetable peeler. Cut eggplants in half lengthwise. Score eggplant pulp in a crosshatch pattern. (Do not cut through the skin. This will make it easier to remove pulp after it is baked.) Brush eggplants with 1 tablespoon of the canola oil, and place in a 13- x 9-inch baking dish. Bake in preheated oven 40 minutes. Remove pulp from eggplants, using a serrated tomato corer or melon baller, leaving a 1/2-inch shell intact. Set shells aside. Coarsely chop pulp, and place in a medium bowl.
Heat remaining 1 tablespoon oil in a small skillet over medium-high. Add onion to skillet; cook, stirring occasionally, until tender, 5 to 6 minutes. Add thyme, garlic, and salt to skillet; cook, stirring constantly, 1 minute.
Add onion mixture and chopped tomato to eggplant pulp. Add eggs, basil, shredded mozzarella, and 1/2 cup of the breadcrumbs; toss to coat. Coat a 13- x 9-inch baking dish with cooking spray. Spread 1/2 cup of the pasta sauce in bottom of dish. Place eggplant shells in dish. Divide tomato mixture evenly among eggplant shells. Top with remaining 1 cup pasta sauce and 1/4 cup breadcrumbs. Sprinkle with torn mozzarella and Parmesan.
Bake eggplants in preheated oven until cheese is melted and top is browned, 35 to 40 minutes. Top eggplants with basil leaves.
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