SPARQL is a query language, that is, a language for formulating questions in. Reasoning, on the other hand, is the process of deriving new information from existing data. These are two different, complementary processes.
To retrieve information from your ontology you use SPARQL, yes. You can do this without reasoning, or in combination with a reasoner, too. If you have a reasoner active it means your queries can be simpler, and in some cases reasoners can derive information that is not really retrievable at all with just a query.
Reasoners like Pellet don't really answer queries, they just reason: they figure out what implicit information can be derived from the raw facts, and can do things like verifying that things are consistent (i.e. that there are no logical contradictions in your data). Pellet can figure out that that if you own a Toyota, which is of type Car, you own a Vehicle (because a Car is a type of Vehicle). Or it can figure out that if you define a pizza to have the ingredient "Parmesan", you have a pizza of type "Cheesy" (because it knows Parmesan is a type of Cheese). So you use a reasoner like Pellet to derive this kind of implicit information, and then you use a query language like SPARQL to actually ask: "Ok, give me an overview of all Cheesy pizzas that also have anchovies".
APIs like Jena are toolkits that treat RDF as an abstract model. Which syntax format you save your file in is immaterial, it can read almost any RDF syntax. As soon as you have it read in a Jena model you can execute the Pellet reasoner on it - it doesn't matter which syntax your original file was in. Details on how to do this can be found in the Jena documentation.
