Rob Purdie played in the win over Torquay United on 1 February but Hereford had missed the previous day's deadline for player registration. Their opponents that day also fielded an unregistered player and have been docked one point.
Hereford currently lie 19th in League Two with 46 points following their goalless draw with Wycombe Wanderers on Tuesday night. The FA's ruling however will drag them back onto 43 points and below Northampton on goal difference if it is upheld.
Hereford chairman David Keyte told the Bulls website: "I'm very disappointed at the outcome, we will definitely be appealing the decision."