Farnborough have been deducted five points after an FA panel upheld a Football Conference misconduct verdict against the club.
Boro are now four points above the relegation zone, with two games left.
Boss Spencer Day said: "I am very disappointed that potential relegation is being decided off the pitch."
He added: "However, I accept the Football Association's decision. It has always been our intention to build bridges both on and off of the pitch since we arrived at the club late last year and we will continue to do so.
"It is particularly difficult on our playing squad who have achieved the 48 points, and we now must lift the players for the vital last two matches.
"We will give it a concerted effort to avoid relegation and not let history drag us down due to no fault of our own."