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The incident was missed by match officials at the time but has since been considered by the video advisory panel.
Hasselbaink has 14 days to respond and faces a possible three-match ban if found guilty of the offence.
The FA also announced that Hasselbaink's team-mate Mario Melchiot will serve a three-match ban after his appeal against his dismissal against Spurs was turned down.
Melchiot's offence was raising an arm to Spurs' Teddy Sheringham in a melee during the Worthington Cup semi-final second leg.
Referee Mark Halsey mistakenly red-carded Hasselbaink as the culprit but the dismissal was later transferred to Melchiot by the FA.