The Nigerian Football Federation (NFF) polls in the southern city of Warri were also delayed for several hours by the detention of election chief Samson Ebomhe.
After reportedly being quizzed by agents from Nigeria’s main intelligence branch, the Department of State Services, Ebomhe returned to the conference hall to announce that the leading candidate, Shehu Dikko, would be removed from the ballot.
Dikko had been favoured to take over the NFF, which has been plagued by a series of controversies since the end of the World Cup in Brazil and sanctioned by FIFA.
The businessman, who helped arrange a tour of Nigeria by Manchester United in 2008, is thought to have powerful enemies in Nigerian politics.
But the reasons for his last-minute disqualification were not immediately clear.
Ebomhe told AFP that Dikko was removed because he was “absent” from the conference.
Pinnick, the president of the Delta State football association in the country’s south, went on to receive 32 votes of the 44-man congress.
His top priority will be deciding on the fate of national coach Stephen Keshi, who led the Super Eagles to the knock-out stage of this year’s World Cup but does not yet have a new contract.
But he may yet have to face further questions from world governing body FIFA about the circumstances surrounding his election.
FIFA had warned that the African champions would face a ban until May if election procedures were not followed.
Football’s governing body first sanctioned Nigeria after security agents arrested outgoing NFF President Aminu Maigari when he returned from Brazil in July.
Maigari was impeached by some of his executive committee members on corruption charges.
FIFA then imposed an international ban on the grounds of political interference after a court sacked the NFF high command and the sports minister imposed a civil servant to take temporary charge.
The ban was lifted after nine days and Maigari was reinstated because his dismissal did not follow laid-down procedures.
But in August, the secret police detained him again, preventing him from attending an executive committee meeting where the owner of Nigeria Premier League side Giwa FC, Chris Giwa, took charge.
That prompted Nigerian referees, clubs and players to boycott the domestic leagues and FIFA to threaten to again suspend the African champions if Maigari were not reinstated and fresh elections held.
Maigari did not contest Tuesday’s vote.