Both children are immediately affected by the verdict, which is given in chapter 21:
I shut my eyes. Judge Taylor was polling the jury: “Guilty… guilty… guilty… guilty…” I peeked at Jem: his hands were white from gripping the balcony rail, and his shoulders jerked as if each “guilty” was a separate stab between them.
Scout and Jem have a physical reaction to hearing Tom's guilt pronounced to the court. Because the evidence was solidly in his favor, they had not expected the jury to return such a verdict of injustice.
Jem doesn't even make it out of the courtroom before breaking down:
It was Jem’s turn to cry. His face was streaked with angry tears as we made our way through the cheerful crowd. “It ain’t right,” he muttered, all the way to the corner of the square where we found Atticus waiting.
This shows that Jem truly believed that his father's excellent defense was enough to convince anyone of sound mind that Tom could not possibly have committed the crimes he was...
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