Huebner was alleged to have used a racist insult against German-born Amiri, whose parents are from Afghanistan, after the pair argued following Union's 1-0 Bundesliga win in the capital last Friday.
But the DFB said "no evidence of a racially motivated or discriminatory act could be provided" and instead banned Huebner for "unsportsmanlike conduct".
"Even Nadiem Amiri could not rule out during the investigations that the choice of words was different," the DFB said in a statement.
The disciplinary committee said both players had apologised to each other for their "respective misconduct".
Huebner said in a statement on the Union Berlin website that he was "glad that the matter has been settled quickly".
"It is of fundamental importance to me that the sports tribunal and the German FA assume that I myself had previously been verbally attacked and that my comments were not discriminatory or racist in any way," he added.
"Any kind of xenophobia and discrimination is deeply abhorred in my family and by me.
"I have spoken to my opponent Nadiem Amiri and we have cleared everything up. This also includes admitting a mistake to each other."
The 29-year-old will miss Saturday's game at mid-table Augsburg and the home game against Borussia Moenchengladbach on January 30.