It is important not to neglect the last two words of the title: "But Waits."
An important element of the story is that the truth comes out, but only after waiting a long time. The reader knows from the very beginning that Aksionov is innocent; a clever reader also figures out fairly early that Makar Semyonich must be the real villain. Justice, however, is not arrived at until the very end of the story, when--years later after the crime--Makar confesses and Aksionov dies a contented man.
The "moral" of the story is debatable. Is Tolstoy saying that we must have faith that God will eventually bring justice to every situation? Or is he cynically pointing out that justice sometimes arrives too late? That is for you, the reader, to decide.