The kit costs £65 and was not released until late on in order to increase demand and reduce the spread of replicas being produced ahead of the World Cup.
The Nigeria Football Federation, which has often complained that counterfeit sales undermine sponsorship deals with partners like Nike, explained that it had received three million pre-orders for this year's kit.
Nigeria will also play in London this week as they face England in a friendly at Wembley as part of World Cup preparations.
Fans of the national team told the BBC they went to the London store after hearing the kit was sold out online.
In a poll conducted by Sky Sports, it was voted the best World Cup jersey. Nigeria's World Cup group contains Argentina, Iceland and Croatia this summer in Russian Federation.
The official Nike Super Eagles campaign is mind-blowingThe Russia 2018 World Cup is just around the corner and so is the release of the official Nigeria jersey.
Rahman Noodles tweeted: "I'm pissed off!"
Another added: "Someone buy me the new Nigeria kit please". That's more than Manchester United's shirt sold in the entirety of 2016.
The shirts, of varying quality, were being sold for as little as $5.
Click through the gallery above to see all the kits of the teams in Groups A to D, and let us know which one you like the most in the comments section below.
But it sold out just moments after going on sale after it was lauded for being the best jersey to be worn in Russian Federation. Most Nigerians I don't think can afford the original.