Teams are only allowed five foreign players on the pitch at a time but Rangers fielded six earlier this month leading to a three point penalty that dropped them into the automatic relegation positions.
A court in the city of Talca, where Rangers are based, ordered the suspension of the promotion/relegation play-offs that the team would have played had they not had the points docked.
However, the ANFP also suspended the title semi-finals and notified FIFA, who do not approve of civil or government intervention in football matters.
"We are communicating the fact and asking FIFA to apply the sanctions it deems appropriate according to its statutes," ANFP general manager Carlos Morales told Bio Bio radio.
Possible penalties include Rangers being banned from the Chilean league.
LAST-FOUR COMPLETE
Elsewhere, the last-four line-up was completed after a high-scoring night of quarter-final, second leg action with Santiago Morning qualifying to face Universidad Catolica and Colo Colo booking a meeting with La Serena.
Santiago Morning were losing 2-0 away to Audax Italiano and on their way out on the away goals rule after seeing their 4-2 first leg advantage wiped out.
Coach Juan Antonio Pizzi sent on reserve goalkeeper Victor Loyola as a substitute striker with eight minutes remaining and he pulled one back with a header three minutes into stoppage time for a 5-4 aggregate win.
Colo Colo beat Universidad de Concepcion 4-3 at home to go through 6-4 on aggregate. Striker Gabriel Vargas scored a hat-trick for the losing side.
Universidad Catolica and La Serena qualified for the semi-finals on Tuesday.
