The Super Eagles B team dominated the early exchanges with Emem Eduok, Samad Kadiri and Musa Mohammed looking lively with their mazy runs at the defence of the Europa League winners.
Kadiri produced the first shot on target in the game racing through to meet a through pass from Muhammed, but he failed to have sufficient elevation on the ball which made it easy for Jan Oblak to block his effort with his big body frame.
Arsenal midfielder Kelechi Nwakali who was out on loan last season to VVV Venlo and later MVV Maastricht both in the Netherlands opened scoring for the Nigerian side with a screamer in the 31st minutes.
Atletico Madrid drew level two minutes later when Eduok was caught in possession by Thomas Patey who slide in Angel Correa and the forward buried his effort past Femi Thomas in goal for Nigeria to bring scores to 1-1.
The introduction of Fernando Torres galvanised the attack of the of the Europa League winners and the former Liverpool, Chelsea and AC Milan hitman deservedly put his side back up.
Torres headed home a corner kick flung into the box of Nigeria to put Atletico Madrid 2-1 up in the 63rd minutes. The goal came six minutes after Thomas was forced into making three saves within a space of three minutes.
Just when it seems Atletico Madrid were going to run out as winners, Sarpsborg of Norway forward Usman Mohammed showed quick feet to take his man out, not once but twice in the box before slotting home the leveller for Nigeria.
Five minutes from full time Borja Garces scored what ended as the winner when he thundered home a ferocious effort from inside the box of Nigeria past Femi Thomas to give his side a 3-2 win.