The case had been brought by Chris Giwa, who was appointed to head the Nigeria Football Federation (NFF) in controversial circumstances in August but then later ousted.
A judge in the central city of Jos had last week ruled that the appointment of a new president, Amaju Pinnick, and executive committee should be set aside.
But a fresh hearing on Thursday was told that Giwa had now withdrawn his complaint.
“I have struck out the matter… The suit ceases to have life,” said judge Ambrose Allagoa.
Giwa’s lawyer Habila Ardzard said the decision had been made “as a result of pleas from so many well-meaning Nigerians and in the national interest”.
Joshua Onoja, representing the NFF, also confirmed that the case had been discontinued.
Football’s world governing body FIFA had given African champions Nigeria until midday on Friday to overturn the court ruling and reinstate Pinnick or face a ban from international competition.
The threat came because FIFA statutes prevent football issues from being heard in a civil court.
FIFA has in recent months repeatedly warned Nigeria that it faced sanctions over the running of the NFF and its handling of elections to appoint a new president and executive committee.