Declan Fitzpatrick appeared in both the 1-0 win over Albion Rovers on Saturday 16 February, and the 1-1 draw with Queens Park the following weekend.
After a disciplinary hearing both matches were awarded to the opposition and the four points were wiped from Clyde’s overall total.
They were also hit with a £1500 fine, £1000 of which is suspended until next summer.
The SPFL decision has massive ramifications for the League Two title race with Danny Lennon’s side having previously sat seven points off leaders Peterhead with a game in hand.
Clyde will have seven days to lodge an appeal.
Chairman David Dishon said in a statement on the Clyde website: “We are deeply disappointed with the outcome of yesterday’s hearing as, despite the fact that we admitted the breach of the SPFL rules, we feel that we put forward a robust and cogent case as part of our defence. The case concerned a player, Declan Fitzpatrick, who has been registered with Clyde since September 2018 and was recently on loan at Clydebank.
“The breach occurred as a result of a genuine oversight and a gap in the administrative procedures. This error was not the fault of any individual.
“We feel that the sanction imposed was unprecedentedly harsh.
“As a result of yesterday’s outcome, we have instigated a full review of our roles & responsibilities and logistics in match day operations and we have put in place additional checking procedures to ensure there is no repeat of this breach.
“I understand that the supporters will share our devastation at this news, but we have to try to stayed focused on the rest of the season. For that reason, the board and I have rejected the offer of two directors to resign from their position.
“Promotion is still a realistic target and that remains our priority. We will continue to give the management and the players our support as they push for promotion.
“The club now has seven days to decide whether or not to appeal the decision and we will take stock over the weekend and consider our next action. We will make no further comment until the end of this process.”