Athletics Kenya (AK) announced the sanction on Friday following a disciplinary hearing held earlier this month in Nairobi, where her estranged partner, Noah Busiendich, Italian manager Federico Rosa and Italian coach Claudio Berardelli all testified.
Jeptoo, the biggest name in Kenyan athletics to have failed a drug test in recent years, tested positive for the blood-booster EPO in an out-of-competition test in September 2014.
The 33-year-old is suspended from all competition until October 29, 2016 with the sanction effectively ruling her out of this summer's world championships in Beijing, China and the 2016 Olympic Games in Rio de Janeiro, Brasil.
However, Rita Jeptoo has the right to appeal her sanction to the Court of Arbitration for Sport.
The two-year penalty is the maximum for a first violation specified by the old World Anti-Doping Agency code, which was in effect when she tested positive last year, but was doubled in the new code that went into effect on January 1, 2015.
Meanwhile Chinese and Norwegian anti-doping officials are in Nairobi this week to help set up the new Kenyan Anti-Doping Commission.