Bruno denies knowing Shmuel when they are caught in the kitchen.  Bruno had given Shmuel some food and Lt. Kotler had caught them.  Shmuel tells the truth and says that Bruno gave him the food, but when Bruno is asked, he just says,

"I...he was here when I came in," said Bruno.  "He was cleaning glasses..." (pg 172)

He knows that he did wrong not to acknowledge Shmuel.

"He had never felt so ashamed in his life; he had never imagined that he could behave so cruelly.  He wondered how a boy who thought he was a good person really could act in such a cowardly way towards a friend." (pg 174)

It is seven days before he sees Shmuel again.  Bruno apologizes to Shmuel and notices that there is a lot of bruising on Shmuel's face.  In his innocence, remember he is just a child, he asks Shmuel if he fell off his bike.  He asks Shmuel if it hurts and Shmuel tells him,

"I don't feel anything anymore." (pg 175)

With that Bruno apologizes to Shmuel again.

"I'm very sorry Shmuel...I can't believe  I didn't tell him the truth.  I've never let a friend down like that before. Shmuel, I'm ashamed of myself" (pg 175)

When he offered this apology, Shmuel smiled and nodded.

"Bruno knew he was forgiven" (175)

After that Shmuel did something that he had never done before.  He lifted the bottom of the fence up and stuck his hand out under it.  He and Bruno shook hands and smiled at each other.  This was the first time they ever touched.