The football bosses had been facing a raft of accusations including over the alleged theft of $8.4 million (7.6 million euros) paid by FIFA for Nigeria's participation at the 2014 World Cup in Brazil.
Judge Ijeoma Ojukwu said she had "no choice" but to order the case ditched after the prosecution asked to drop some of the charges.
The government in September dissolved the anti-corruption agency prosecuting the case over its own graft scandal.
The case had been repeatedly adjourned since the football officials were charged in May as they failed to answer summons to appear in court.
The ruling on Tuesday is not the end of Pinnick's troubles as he is facing another potential trial for graft.
Last month the authorities seized a dozen properties from senior officials of Nigeria's top football body, including Pinnick, in a fresh corruption probe.
Anti-graft agents took over 12 properties -- half belonging to Pinnick, including a property in London -- in the latest investigation to target senior football bosses.
Pinnick has remained at the helm of Nigerian football's governing body despite the graft allegations.
He was sacked as vice-president of the Confederation of African Football (CAF) in July.