Altidore had not scored since December for either his English Premier League club Sunderland or the national team but managed a goal in each half to send the U.S. to Brazil on the back of three successive friendly victories. (Agencies)
Nigeria forward Victor Moses spoiled U.S. keeper Tim Howard's hopes of a clean sheet in his 100th international appearance with a late consolation from the penalty spot.
U.S. coach Juergen Klinsmann selected two holding midfielders to address the defensive shortcomings in his side's 2-1 win over Turkey last Sunday.
Real Salt Lake's Kyle Beckerman paired up with Jermaine Jones behind Michael Bradley and Alejandro Bedoya. The result was a disciplined performance against a Super Eagles team that passed the ball efficiently in midfield before losing their sense of urgency in the final third.
Nigeria enjoyed the territorial advantage in the early stages with Chelsea's Mikel John Obi serving as the midfield fulcrum. Moses found a yard of space behind a packed U.S. defense before Geoff Cameron's recovery forced him to pull his shot wide of the near post.
A purposeful U.S. counter-attack in the 23rd minute saw Bradley collecting Clint Dempsey's flick before testing Nigerian goalkeeper Victor Enyeama with a 25-yard shot. Bedoya's curling effort from the resulting corner kick sailed over Enyeama's crossbar.
Altidore broke the deadlock, and his lengthy dry spell, with a tap-in in the 32nd minute. Fabian Johnson thundered to the bye-line before squaring for Altidore to side-foot into an empty net from three yards.
The visitors almost found an equalizer in the closing minutes of the first half when Efe Ambrose was left unmarked at a corner kick but Howard smothered the Glasgow Celtic defender's header at his near post.
Dempsey and Bradley combined to great effect again on 65 minutes with a quick exchange that led to the former Fulham player bringing a fine save out of Enyeama.
Altidore doubled the U.S. lead three minutes later with a goal that showed his renewed confidence.
The burly striker brought down a diagonal pass from Bradley and stepped inside Joseph Yobo on the left of the penalty area before smashing his shot inside Enyeama's near post.
Nigeria pulled a goal back on 86 minutes after Matt Besler dragged Moses to the ground inside the area and he rose to coolly slot the spot kick.
The U.S. team leaves for their World Cup base in Sao Paolo on Sunday and begin their Group G campaign against Ghana on June 16 with games against Portugal and Germany to follow. Nigeria meets Iran, Bosnia and Herzegovina and Argentina in Group F.
Altidore had not scored since December for either his English Premier League club Sunderland or the national team but managed a goal in each half to send the U.S. to Brazil on the back of three successive friendly victories.