Combine tomatoes and shallots with 1/2 teaspoon salt in a blender, and puree. Heat 2 tablespoons oil in a medium nonstick skillet over medium-high heat. Add the tomato mixture, and simmer until reduced slightly, about 2 minutes; set aside.
Heat remaining tablespoon oil in a medium nonstick skillet over medium-high heat. Add 1 tortilla, and cook until bubbles form and edges begin to brown, 30 to 45 seconds. Turn, and cook for 10 seconds more. Drain on paper towels. Repeat with remaining tortilla. Place 1 tortilla on each of two plates.
If necessary, add a bit more oil to pan. Crack the eggs into the skillet, and cook sunny-side up (until whites are set and yolks are still soft), about 2 minutes. Slide one egg onto each tortilla.
Spread sauce around eggs so that the sauce covers the entire white, leaving only the yolk showing. Sprinkle with salt and pepper, and garnish with cilantro and jalapeno. Serve immediately.