The most important symbols in this short story are Aksionov's house (and two shops) and the Siberian prison mine where he is sentenced to hard labor.
When Aksionov is first introduced to us, he is described as a 'handsome, fair-haired, curly-headed fellow, full of fun, and very fond of singing.' However, the protagonist of Tolstoy's 'God Sees The Truth, But Waits' undergoes a spiritual transformation in the story.
His house and two shops represent his family, his material possessions, and his earthly affairs. Aksionov's wife visits him when he is initially imprisoned in the nearest town; having been accused of murdering the merchant who shared an inn room with him, Aksionov can only wait for his fate. When his own wife doubts his innocence, he is devastated. At this point in the story, we see that Aksionov is starting to realize that he can no longer trust in any of the things he has depended on in his life; he cannot depend on his material wealth to prove his innocence and sadly, he also cannot depend on the woman he is married to for loyalty in a time of great need.
In prison, we are told that
His hair turned white as snow, and his beard grew long, thin, and grey. All his mirth went; he stooped; he walked slowly, spoke little, and never laughed, but he often prayed.
The prison itself is a symbol of his suffering and his eventual spiritual transformation. When Aksionov realizes that Makar was the one who framed him for the merchant's murder, he suffers all the mental agonies of the wronged: should he now expose Makar (for his tunnel-digging escape project) and enjoy a belated revenge for all the sufferings of the last twenty six years? Well, Aksionov eventually decides that he's going to let bygones be bygones. He refuses to incriminate Makar. Makar is so touched that he confesses everything to Aksionov and begs for forgiveness. Through this simple act of forgiveness, Aksionov is finally able to obtain peace. His focus is now towards the eternal:
When Aksionov heard him sobbing he, too, began to weep. "God will forgive you!" said he. "Maybe I am a hundred times worse than you." And at these words, his heart grew light, and the longing for home left him. He no longer had any desire to leave the prison, but only hoped for his last hour to come.
Hope this helps!