André Gleißner died along with four adult women when a car drove through Magdeburg's Christmas market on Friday.
Women, aged between 45 and 75, were also killed in the attack, which left 200 others injured.
Taleb al-Abdulmohsen, a 50-year-old doctor who arrived in Germany in 2006, is being held on suspicion of the attack and appeared in court on Saturday night.
Germany was warned "four times" about the extremist views of the Magdeburg car attack suspect, Saudi officials say.
Abdulmohsen has been charged with five counts of murder and a number of counts of attempted murder.
Writing on Facebook, André's mother Désirée wrote: “Let my little bear fly around the world again. André did nothing to anyone. He was with us on earth for only nine years. Why you? Just why?
"I don't understand. Now you are with grandma and grandpa in heaven. They have missed you so much, as much as we miss them here now. You will always live in our hearts. I promise that.”
Hundreds of thousands of people paid tribute to the little boy and one person who knew the family wrote: "It is incomprehensible. André was just a little angel to everyone. He has enriched so many people in his short life with his kind nature and so much zest for life.