Khaled Abdulaziz Al Eid, individual bronze medallist at the Sydney Olympics, and Abdullah Waleed Sharbatly, individual silver medallist at the world equestrian games in 2010, were given eight-month bans backdated to February.
Their horses Vanoeve and Lobster 43 tested positive for the non-steroidal anti-inflammatory drugs phenylbutazone and oxyphenbutazone which are listed as controlled medication substances.
"Controlled medication substances are those that are prohibited in competition, but are permitted for treatment use outside competition," said the FEI.
"The rules provide that the suspension period for controlled medication substances can be anywhere between a warning and two years."
The FEI said that Al Eid had failed to prove that ingestion by means of exposure to a contaminated stable environment was the likely source of the prohibited substances found in the horse's system.
Abdullah Waleed Sharbatly had failed to establish how the prohibited substances entered the horse's system.
The riders can still appeal to the Court of Arbitration for Sport.