Mr Kelner, who was madeeditor of the paper last May, was nominated by the journalists who presented BBC2's What the Papers Say programme during its last series.
The judges said: "He stabilised the paper's circulation figures; other journalists have greatly admired the way he so swiftly stopped the rot. They nominated him in great numbers and the judges agreed."
The Independent also took the Correspondent of the Year prize for the work of the Ireland correspondent, David McKittrick. The judges said: "Nowhere could you find a better route map of the troubles of Northern Ireland than in the articles of The Independent's David McKittrick".
Other awards included a new category of Front Page of the Year, which was won by The Sun, for its headline, after the arrest of the singer George Michael in a Los Angeles public lavatory, which said: "Zip me up before you go go".
The Columnist of the Year award went to Libby Purves of the Times. The Peter Black award for writing on broadcasting went to the Daily Mail's Jaci Stephen. The judges said she was such a genuine enthusiast for her subject and could be so funny. "She has charm with teeth."
The Guardian's Nick Davies won Journalist of the Year forhis "frankly terrifying reports on life in hidden Britain", included stories on the web of paedophiles who abused children in institutions in the north of England. The paper also won Scoop of the Year for its story about Peter Mandelson's home loan arrangement withGeoffrey Robinson.
Hosted by Clive Anderson, the What The Papers Say awards will be shown at 7.35pm today on BBC2.