In the wake of his side's 1-0 defeat at Old Trafford on January 16, the 58-year-old was charged for a breach of the Football Association's Rule E3, suggesting he had questioned the integrity of officials or implied that they were motivated by bias.
At the time he was unhappy that Manchester United had been awarded a penalty while his side were not, in relation to two handball incidents.
Allardyce said: "You see it time and time again at Old Trafford.
"There's no doubt about the difference between Rafael's handball and Jordan Spence's.
"Spence plays for West Ham and the away team, while Rafael plays for the home side at Old Trafford."
The FA confirmed the details of Allardyce's fine on Wednesday afternoon after he had been to a personal hearing, as well as warning him about his future conduct.