It's because "engines" is a plural and the sentence is comparing. It sounds less natural but you could say: A diesel engine is usually more fuel-efficient than a petrol one

Don't confuse the noun with the adjective. In your sentence, 'ones' is used in place of 'engines' in order to avoid repetition. Here are more examples: I usually order the double-beef hamburger, but today I'm not very hungry so I'm going to order the single one. My friend likes to wear a fancy dress to parties but I prefer to wear a simpler one. 'Ones' is also used as a possessive pronoun referring to someone in general. One (subject pronoun) should obey ones (possessive pronoun) parents.