The Hoops boss was brought to task after television microphones picked up comments aimed at St Mirren defender Jim Goodwin during a game in March.
Goodwin defended Lennon over the verbal exchange, and the incident was not noted by the fourth official at St Mirren Park, but the SFA has instead decided to act as the result of two complaints from television viewers.
A statement from Celtic read: "Clearly we are extremely surprised and disappointed by today's decision.
"Fundamentally the particular disciplinary system in place is absurd - a system where such a case can be brought on the strength of two 'complaints' from people totally unconnected to the match in question, while a fourth official overseeing the technical area during the match makes no mention of any incident to the SFA.
"Despite even supportive comments from numerous individuals including Jim Goodwin himself, this judgement has been made, something which we find quite astonishing.
"It is clear that this decision will have huge repercussions for the game in Scotland and we are sure Hampden Stadium will be a very busy place now every Monday morning."
The Celtic boss has five days to appeal the decision, and is likely to do so on Friday - which means he will be in his usual spot for Sunday's match against Inverness Caley.