You pond the pilings down until you hit bed rock.
Suppose the bedrock is 100 feet down. It does not seem possible that a skyscraper could be built on 100 foot long legs, no matter how thick they were, without any cross-bracing. So the fill does have something to do with supporting the building.
According to some answers from engineers on Quora, foundations of skyscrapers do not always go to bedrock.
One of the piers of the Brooklyn Bridge does not go all the way to bedrock and yet it has stood for over 133 years.