"FIFA can confirm that this match between Nigeria and Argentina was one that we had an active interest in, and forms part of a wider ongoing FIFA investigation," said FIFA in a statement.
"In particular, FIFA will be working closely with colleagues at the FIFA early warning system."
Refereree Ibrahim Chaibou of Niger awarded two controversial penalties in the match, Victor Obinna converting for Nigeria in the 27th minute and Mauro Boselli scoring for Argentina deep into stoppage time with the last kick of the match.
Manipulation of matches by gambling rings has become a major concern for world soccer's governing body FIFA and its European counterpart UEFA and both monitor thousands of matches for unusual betting patterns.
Last month, FIFA set up a partnership with Interpol and announced it would donate 20 million euros over the next 10 years to fight the problem.
FIFA is currently investigating two international friendlies played in Turkey in which seven penalties were awarded, one of them taken twice. The six match officials involved have been suspended pending the outcome.
FIFA has already tightened the rules around the arrangement of international friendlies.
Both FIFA and UEFA say that match-fixers tend to target lower-profile matches - often in the early qualifying rounds of European competition, lower division of national leagues or obscure international friendlies - to avoid attracting attention.
Wednesday's match was played on the same day as Sepp Blatter was re-elected as FIFA president in Zurich and emphasised a "zero tolerance" policy towards corruption.
Argentina sent a B team to the match in the Nigerian capital Abuja and the outcome also prompted Argentine FA president Julio Grondona to criticise his national team coach Sergio Batista.
"Batista asks for these matches, you can't (take) a risk like that," said Grondona, referring to Batista's decision to take a second-string team.
"One level is not the same as the other, Nigeria picked their best players."
