World football's governing body said in a statement that Tajikistan would be reinstated into the competition in Syria's place.
"The Syrian team is disqualified from the competition, losing their second round knockout phase by forfeit," FIFA said in a statement.
"These decisions are final and binding and not subject to appeal."
FIFA said the same ineligible player, who has not been named, had taken part in both legs of Syria's Asian qualifying second round tie against Tajikistan on July 23 and 28 and a 3-0 defeat had been imposed on them in each match as punishment.
When the matches were played, Syria had won 6-1 on aggregate.
Syria, who have never reached a World Cup finals, were not expected to reach the 2014 edition in Brazil.
Tajikistan will now play in the third round of qualifying, where they are in Group C with Japan, Uzbekistan and North Korea. Their first game in this stage will be at home to Uzbekistan on September 2.
Sherali Davlatov, general secretary of the Tajikistan Football Federation, said justice had prevailed.
"It was a correct decision and we're very happy to be reinstated," Davlatov told Reuters from the Central Asian country's capital Dushanbe.
"We feel FIFA has done justice to Tajikistan and especially to our fans. The Tajik fans will be delighted to see our team playing against some of the continent's major sides, such as Japan, Uzbekistan and North Korea," he added.
"Most people will regard us as outsiders but it's not to say we don't have a chance against any of them because football is often so unpredictable."
The Syrian football association was not immediately available to comment.
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