My 2 year old eats tomato without a problem; this time a rash appeared on his face from where it touched him. Does this mean he is allergic to it?

Possible allergy. You don't want to jump to conclusions, but it sounds very suspicious for development of an allergy. There are many different types of tomatoes, so it may not be to all of them. It also might be a preservative or other coating on the tomato that he was sensitive to. Seeing an allergist can confirm or rule out an allergy. Otherwise, be careful if giving tomatoes or tomato based sauces.