Anti-discrimination body FARE reported the singing of an abusive song directed at the Ferdinand brothers during the World Cup qualifier at the Olympic Stadium in Serravalle.
However FIFA has said it will not take any action due to a lack of evidence, although the FA has been warned to take "preventative measures".
A FIFA statement said: "We can confirm that in the case of alleged racist chanting during the recent World Cup qualifier San Marino vs England, it has been decided not to open disciplinary proceedings due to the lack of concluding evidence.
"The FA's attention was however drawn on the pertinent provisions of the FIFA regulations and they were requested to display prudence and adopt appropriate preventive measures in order to avoid that incidents of such nature do occur in the future."
Rio Ferdinand had incurred the anger of some England fans after pulling out of the international squad at short notice, but the fact that his brother Anton was also allegedly targeted raised concerns given that he was the victim of racist abuse by former England captain John Terry last year.
The FA wrote to FIFA last month to say it had found no evidence of the racist chanting but did not dispute that it had taken place.