A team official has also been given a 30-day ban in connection with the June 11 match which Jamaica lost 2-0 in Tegucigalpa, world football's governing body said.
FIFA said it had opened disciplinary proceedings and the player and official have been given until August 19 to submit a statement and supporting evidence.
The Jamaica Football Federation (JFF) said on July 25 that it had been informed by FIFA about "an adverse analytical finding on his urine sample".
FIFA said its own regulations prevented it from giving any further details.
"Only after it has been determined in a hearing that an anti-doping violation has occurred may FIFA publicly report the anti-doping rule violated, the name of the player or other person who committed the violation, the prohibited substance and the consequences imposed," it said.
Jamaica, whose only World Cup finals appearance was in 1998,are bottom of the six-team group in the final stage of the CONCACAF World Cup qualifying competition with two points from six games.
Jamaican athletics has been rocked by a doping scandal with several testing positive for banned substances, including twice Olympic 200 metres champion Veronica Campbell-Brown and former world 100 metres record-holder Asafa Powell.
Peru midfielder Joel Sanchez was banned for two years by FIFA after failing a doping test in a World Cup qualifier in Bolivia last October.