Peer-review is the key distinction between scholarly and non-scholarly sources.
In contrast to popular newspapers, magazines, websites, and books, scholarly sources are written by experts in a particular field and then reviewed (assessed, evaluated, etc.) by other experts in that field prior to publication.
Few databases (ex. JSTOR) include only scholarly sources. Usually databases include a mix of popular and scholarly material.
Some databases let you limit your search to only scholarly, peer-reviewed materials. Look under the Limits or Filters section on the database's search screen for the words "scholarly journals" or "peer-reviewed".
In EBSCO Academic there is a checkbox under the Limits section for "Scholarly (Peer Reviewed) Journals".
In ProQuest Direct there is a checkbox for limiting to "Peer reviewed" materials.