Rafael was sent off after being booked for a foul on Benoit Assou-Ekotto- he had been cautioned earlier in the match.
Anger management: Rafael Da Silva screams at referee Mike Dean after his dismissal
The FA said in a statement: 'Manchester United defender Rafael Da Silva has today been charged by the FA with improper conduct.
'The charge relates to the player's conduct towards match official Mike Dean following his dismissal in Manchester United's fixture at Tottenham.'
The United player has until 6pm on Tuesday to respond to the charge.
Sir Alex Ferguson's long-running feud with Dean erupted again after Rafael was given a second yellow card for tangling legs with Assou-Ekotto.
Ferguson said: 'It's not worth discussing because everyone can see that. It's out of my bounds now. Thank God.'
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