Developers' marketing budgets are presently spent on social media or online adverts, he argued, where they were less effective.
The move comes ahead of Apple's Worldwide Developer Conference in San Francisco next week, where it is expected to preview new software for the iPhone and Apple Watch, and possibly announce a new home device and updates to its MacBook Pro laptops.
Mr Schiller said with "so much" to announce next week, Apple wanted to tell developers about the App Store changes ahead of time.
The single ad appearing above the "organic" results will be marked as an advert and appear on a blue background. The chosen ad will be determined by a "relevance" metric.
"If you're searching for sports cars, you shouldn't get an ad for pretty ponies," said Mr Schiller. Ads can only be for other apps inside the store and developers will only have to pay if the ad is clicked on.
James Thomson, author of the iOS calculator app Pcalc and Mac OS app DragThing, said paid search "is a terrible idea for indie [independent] developers and will only benefit the big companies with deep pockets, rather than users. It will make the playing field even less level. Search should return the best and most relevant results, not the results with the biggest marketing budget."
Dave Verwer, an independent iOS developer, said: "Apple has a huge amount of data not only on the apps we buy, but on those that we use," and suggested search recommendations should be built on that.
However, Mr Schiller said having use-based recommendations would favour the larger, already-established apps, and wouldn't give new or small apps a chance to break through.
The other key change will see app developers earn more from subscriptions if they keep customers signed up for more than a year. After the first year of a subscription, Apple will halve its 30 per cent slice of the payment to 15 per cent, where it will stay. Developers will be able to change the subscription fee, which the subscriber will have to approve; if they do not, the subscription will lapse.