Altidore scored his first goal in 2014 for club or country just after the half-hour mark, tapping in Fabian Johnson's cross, while he added a second after half-time to ensure the USA completed their FIFA World Cup preparations with three wins from as many games.
By contrast, Nigeria will head to Brazil having failed to win any of their pre-tournament friendlies with the loss at EverBank Field following draws with Scotland and Greece.
During the USA's pre-World Cup training camp, the American media had regularly questioned coach Jurgen Klinsmann's insistence on playing Altidore at the point of his formation, with the 24-year-old having failed to score in six internationals.
But the powerful striker was clinical against Nigeria on Saturday, scoring both goals as the USA celebrated goalkeeper Tim Howard's 100th cap in style.
Nigeria started better and were keen to get the ball quickly to their forwards out wide in an attempt to get in behind the USA's defence.
The same duo also combined nine minutes later, with Moses' corner finding Ameobi and his header bounced up and had to be tipped away by Howard as the ball looped towards the top corner.
But as the half wore on, Klinsmann's midfield wall of Bradley, Beckerman and Jones began to get on top with Nigeria struggling to break down the USA's disciplined defensive shape.
The 26-year-old Toronto FC midfielder got on the end of a fine attacking move at the midway point of the first half, forcing Nigeria goalkeeper Vincent Enyeama into a low save down to his right, which sparked a period of dominance for Klinsmann's men.
From the resultant corner, Bedoya curled a shot just beyond the top corner of Enyeama's goal and, soon after, another set piece saw Dempsey's acrobatic volley fly over the bar.
Nigeria's best chances in the first half came from corners and in the 44th minute, Howard had to make a save at the near post, although the ball almost squirmed between his legs.
The visitors had more possession in the first half and continued that trend after half-time, although they were unable to penetrate the USA's defence.
Just after the hour mark, the USA reminded Keshi's men of the threat they posed on the counter-attack with Bradley feeding Dempsey and the hosts' skipper stepped inside one opponent only to fire his shot straight at Enyeama.
