The captain of FC Bundestag, Marcus Weinberg, said the AfD's Sebastian Münzenmaier could not be part of the squad because he had been convicted last year and handed a suspended sentence of six months for hooligan violence.
"It's a question of openness to the world, of fair play and tolerance," Weinberg, a member of Chancellor Angela Merkel's CDU party, told AFP's sports subsidiary SID.
But Münzenmaier has protested against the decision, claiming he is a victim of political ostracism by mainstream parties.
"Another good example of the so-called tolerance of the old parties, without discussion or justification, they prefer to take a shower among themselves and refuse to play football with everyone," complained the 28-year-old.
Weinberg argued however that his team did not exclude AfD lawmakers because of their politics.
"Before the start of every legislative period, we write to all the parties to ask if the MPs would be interested to come join the team. That's what we did with the AfD," he said.
The squad took on three players from the far-right party.
FC Bundestag regularly organises matches for humanitarian causes, including an upcoming game against a team of refugees.
Münzenmaier was sentenced last year by a court for having participated in clashes in 2012 between fans of Mainz and FC Kaiserslautern, the team he supports. His appeal is pending.
Capitalising on the public's misgivings over the arrival of more than a million asylum seekers since 2015, the AfD won more than 90 seats during September's elections, triggering a political earthquake in Germany.
Its arrival in the Bundestag has left mainstream parties scrambling on how to deal with its lawmakers - from where they should sit in parliament to which among them should be among vice-chairs at the Bundestag.