Ivan Knyazev and Daria Meshcheryakova have each been banned for two years, while Vladimir Obukhov's period of ineligibility was reduced to six months for admitting the offence and "providing substantial assistance" during the investigation.
A forensic investigation conducted by FIFA and the World Anti-Doping Agency (WADA) found "compelling evidence" of the use of methandienone in the cases of Knyazev and Obukhov, and furosemide in the case of Meshcheryakova.
Methandienone is a prohibited steroid while Furosemide is a banned masking agent.
Forward Obukhov, 29, is a former Russia youth international and played 21 times for Rostov in the country's top flight, while 28-year-old defender Knyazev is a free agent after last playing for lower division side Zvezda Perm.
Goalkeeper Meshcheryakova, 26, also represented Russia at youth level.
"For all three players, the suspension covers all types of matches, i.e. competitive and friendly fixtures, whether domestic or international," FIFA said in a statement.
FIFA said the three cases originated from doping controls taken in 2013 that were analysed in the Moscow laboratory but originally reported as negative in WADA's system.