The International Association of Athletics Federations had appealed to the CAS to increase a two-year ban imposed by Greek officials after Kokkinariou, 31, was found guilty of blood doping in July, based on an abnormal biological passport, or blood profile, between 2009 and 2011.
The CAS agreed with the IAAF that there were aggravating circumstances which merited an increased ban, saying Kokkinariou's blood profile was "conclusive evidence of the repeated use of blood doping over a protracted period of time as well as her engagement in a carefully planned doping scheme".
The ban will run from October 27 last year, the date of Kokkinariou's provisional suspension, and her results would be scratched for the affected period, officials said.
The Greek Athletics Federation (SEGAS) was ordered by the CAS to pay the costs of the appeal.
Kokkinariou finished last in her heat of the 3,000m steeplechase at last year's world championships in Daegu.