Several Watford players reacted angrily to referee Graham Scott's decision to award Ipswich a penalty when he adjudged Gabriele Angella to have handled Frank Nouble's cross in the clash on December 21.
David McGoldrick subsequently scored from the spot to put the hosts ahead in the 73rd minute, before Troy Deeney levelled the scores at 1-1 nine minutes from time in what was new Watford coach Giuseppe Sannino's first game in charge.
Having been charged on December 24, Watford admitted the offence on Tuesday and have subsequently been sanctioned.
A statement on the FA's official website read: "Watford have been fined the standard penalty of £5,000 after admitting an FA charge of failing to ensure its players conducted themselves in an orderly fashion and/or refrained from provocative behaviour.
"The incident occurred in or around the 71st minute of their game against Ipswich Town on 21 December 2013."
Elsewhere, Coventry City's Dan Seaborne has been handed a three-match ban by the FA after admitting a charge of violent conduct for an incident with Oldham Athletic's Jonson Clarke-Harris on December 29 that went unnoticed by match officials.
"Coventry City’s Daniel Seaborne has been suspended for three matches with immediate effect after he admitted an FA charge of violent conduct," a statement from the FA read.
"The incident, which was not seen by the match officials but caught on video, occurred in or around the 42nd minute of his side’s game against Oldham Athletic on 29 December 2013."
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