Favourites New Zealand were expelled from the under-23 tournament final in July for fielding ineligible South African-born defender Deklan Wynne.
The Oceania Football Confederation disciplinary committee took the decision after an appeal by Vanuatu, who had lost 2-0 in the semi-finals to New Zealand.
Fiji went on to beat Vanuatu on penalties in the final in Papua New Guinea to qualify for the men's Olympics football tournament at next year's Rio Games.
New Zealand are still appealing the decision but De Jong opted to stand down from the position he has held since 2012.
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"The issues of eligibility have arisen within the high performance department and as leader of that department I must accept a level of accountability for what's happened," he was quoted as saying by the New Zealand Herald.
"There's a level of accountability that I accept, it's out of my department and that's how accountability is, that's the responsibility of the leader. Within the framework of that it's the right time to step aside and let someone else lead the programme.
"The roles and responsibilities of what happened with the Olympic campaign will come out later in the piece, but right now I'm comfortable with the accountability."
The paper speculated missing out on qualifying for the Rio de Janeiro Games would cost New Zealand Football up to NZ$1.5 million (630,808 pounds), with more spent on legal fees appealing the decision.
(Writing by Patrick Johnston in Singapore; Editing by Ian Ransom)
