Kiffin tweeted the photo Saturday night, a day after the Owls' 36-31 home loss to Marshall. The photo depicts three officials holding German Shepherd dogs in one hand with walking sticks in the other hand, while wearing dark glasses. Kiffin mentioned Conference USA in the tweet.
The conference cited Kiffin for violating the league's sportsmanship policy.
"Conference USA has specific rules and standards regarding sportsmanship which have been adopted by our membership," commissioner Judy MacLeod said in the statement. "We have an obligation to enforce our rules, including the prohibition of public criticism of officiating."
At his postgame news conference, Kiffin told reporters he didn't want to "get into officiating."
"I don't know if we lose money in this conference -- we probably do -- and I don't have a lot anymore," Kiffin said.
The Owls coach told ESPN that Conference USA agreed there were "inconsistencies" in the game's officiating. FAU was flagged for nine penalties for 90 yards in the loss to the Thundering Herd.
"I just lost $5,000 for a tweet," Kiffin told ESPN. "We have freedom of speech, but I guess around here there's no such thing as freedom to tweet."
The Owls (4-3) face Old Dominion at 3:30 p.m. EDT Saturday in Norfolk, Va. Kiffin, 44, owns a 20-13 record in three seasons at FAU. He owns a 55-34 overall record as a college head coach, with previous stops at Tennessee and USC.