Bring a large pot of generously salted water to a rolling boil.
Add the penne and cook according to package directions until al dente, typically 12-15 minutes.
While the pasta cooks, heat 2 tablespoons (30 ml / 1 fl oz) of olive oil in a large skillet over medium-high heat.
Add half of the diced eggplant in a single layer and cook, tossing frequently, until golden brown and nearly tender. The eggplant will absorb the oil quickly; resist adding more and continue tossing to prevent sticking.
Transfer the cooked eggplant to a plate and repeat with another 2 tablespoons (30 ml / 1 fl oz) of oil and the remaining eggplant.
Reduce the heat to medium and add the final tablespoon of olive oil to the same skillet.
Add the minced garlic and red pepper flakes, and sauté for about 2 minutes until the garlic is fragrant and golden, being careful not to burn it.
Stir in the drained diced tomatoes, salt, and a generous amount of black pepper.
Bring the sauce to a simmer.
Return the cooked eggplant to the skillet with the sauce.
Continue to simmer, stirring occasionally, for 7-10 minutes, until the sauce has thickened and the eggplant is perfectly tender.
Just before draining the pasta, reserve about a cup of the starchy pasta water.
Drain the penne and return it to the pot or a large serving bowl.
Pour the hot eggplant sauce over the pasta, add the fresh parsley, and toss everything together until well-coated. If the sauce is too thick, add a splash of the reserved pasta water to reach your desired consistency.
Serve immediately, passing a bowl of grated Parmesan cheese at the table.
Don't overcrowd the skillet when browning the eggplant.
Cooking it in two batches ensures it fries to a beautiful golden-brown rather than steaming, which vastly improves its texture.