Brazil striker Neymar, who scored both goals on Sunday, complained after the game that he had been the target of racist abuse.
Arsenal said London's Metropolitan Police were satisfied there was no racist intent and that no action will be taken against the fan.
"After consultation with the Metropolitan Police, Arsenal Football Club can confirm that a German teenage tourist has admitted throwing a banana onto the pitch during the Brazil v Scotland International Friendly at Emirates Stadium on Sunday," Arsenal said in a statement.
"The youngster was sitting in the North Bank of Emirates Stadium, an area of the stadium which was occupied by the official allocation of tickets to Brazil supporters, when he threw the banana onto the pitch during the second half of the match."