Yevgeny Dzhugashvili said an article published in Novaya Gazeta claiming Stalin personally ordered the deaths of Soviet citizens was a lie.
He had requested a public apology and damages from the opposition newspaper.
But the court rejected his petition. Russian media said its reasons would be made public later.
The Novaya Gazeta had published a piece referring to declassified death warrants, which it said bore Stalin's personal signature.
Mr Dzhugashvili had argued that this was a lie and that Stalin never directly ordered any deaths.
The case was seen by many as part of a Kremlin-backed campaign to rehabilitate Stalin's reputation, correspondents say.
Mr Dzhugashvili has five days to appeal against the ruling.
He was not in court for the verdict, but it was greeted with applause by some present, and shouts of "shame" from others, Russian state-owned news agency Ria Novosti reported.
