Left-hand batsman Ballance, 21, has signed a two-year extension, as has off-spinner Azeem Rafiq, 20.
Right-arm seamer Moin Ashraf, 19, and Joe Root, 20, a right-hand bat and offspin bowler who also enjoyed a breakthrough season, have been offered similar deals.
Yorkshire have also released bowler Ben Sanderson and all-rounder Lee Hodgson, while spinner David Wainwright has exercised the clause in his contract where he can request to be released if he is not playing regular first-team cricket.
Junior pro contracts have been awarded to Alex Lees, 18, and James Wainman, 18, and summer contracts to Callum Geldart, 19, Alex Lilley, 19, and Dan Hodgson, 19.
Director of professional cricket Martyn Moxon said: “We are delighted to offer contract extensions to these very talented youngsters who have shown such promise in an otherwise disappointing season.
“As is the nature of the game, we have also made the very difficult decision to release three other professionals and we wish Lee, Ben and David all the very best for the future.”