Combine tomato and onion in medium baking dish. Roast about 30 minutes or until onion softens. Remove from oven; cool.
Reduce oven to 200°C/400°F.
Meanwhile, preheat grill. Quarter capsicums; discard seeds and membranes. Roast under hot grill, skin-side up, until skin blisters and blackens; cover capsicum pieces with plastic or paper for 5 minutes. Peel away skin; slice capsicum thinly. Place capsicum, cheese and basil in baking dish with tomato mixture; stir gently to combine.
Stack all nine sheets of filo on an oven tray, spraying every third sheet with cooking oil spray. Fold all four sides of filo stack in slightly to form 18cm x 30cm rectangular tart shell. Fill shell with vegetable mixture; bake about 15 minutes or until pastry is golden.