The ban on the Dubai ruler came as a result of his horse Tahhan testing positive in two two-star races for a hypertension drug and the steroid stanozolol.
Sheikh Mohammed was also ordered to pay 4500 Swiss francs in fines and legal costs.
His trainer, Abdullah bin Huzaim, who admitted giving the horse drugs before the desert races at Bahrain and Dubai, was handed a one-year ban.
Under FEI rules, the person riding the horse in an event is responsible for any drug breaches, although other support personnel may also be held accountable if circumstances dictate.
The FEI tribunal, comprising Patrick Boelens, Philip O'Connor and Erik Elstad, said in its decision that Tahhan competed in a 120km race in Sakhir, Bahrain, on January 10 this year and a 120km race in Dubai on February 28, in both cases ridden by the sheikh.
The horse was selected on both occasions for blood testing, and was also routinely tested at his home stable, when the positive tests were returned.
One of the prohibited drugs detected, Guanabenz, is used to treat blood pressure in humans and is known to have a calming and painkilling effects.
The other drug, Hydroxy-Stanozolol, is a metabolite of Stanozolol, which is an anabolic steroid.