Bruce was left enraged when referee Michael Oliver penalised Ahmed Elmohamady for a handball, with Roberto Soldado making no mistake from the resulting penalty at White Hart Lane to score the only goal of the game.
"It's a joke decision," Bruce seethed after the match.
"I shouldn't say this and I might get fined, but would we have got it? I'm not so sure."
The FA have started disciplinary action against the 52-year-old, as a statement on the governing body's website read: "It is alleged Bruce’s comments called into question the integrity of the match referee, and/or implied that the match referee was motivated by bias; and/or brought the game into disrepute, in contravention of Rule E3(1).
"Bruce has until 6pm on November 4 to respond to the charge."
Hull also played Tottenham in the Capital One Cup on Wednesday, again slipping to defeat.
After a 2-2 draw in extra time, Elmohamady was again at the centre of things, missing the crucial penalty as Spurs triumphed 8-7 in the shootout.