The Millers were leading 1-0 through Angus MacDonald's early goal before Crooks was controversially dismissed for an aerial challenge on Grant Hall with 18 minutes played.
The collision forced Hall from the field but Crooks was clearly left puzzled by the call as he was shown a straight red card by referee Darren Bond.
Middlesbrough went on to win the game with goals either side of the half-time break before Rotherham confirmed their intention to appeal the dismissal.
The EFL announced their decision to uphold the original decision on Saturday, with Crooks issuing a response admitting he was "bemused" the red card would stand.
"Bemused by the decision to not overturn the red card I received on Wednesday, possibly more so than I was receiving the red itself," he posted on social media.
"Maybe I shouldn't have such a big head. Maybe I shouldn't jump.
"As an epileptic footballer, of course my thought process on the field of play is to run around at maximum velocity using my head as a bayonet.
"Football is a contact sport and I will probably see a handful of similar well-contested aerial challenges over the course of this footballing weekend.
"Intrigued at what direction the game is going in if that's the standard red card offence.
"I am looking forward to my next game where I shall jump with my hands pinned to my hips and with as little power as my 6ft 5in frame allow me. Game's gone."
Referee Bond has previous history with Rotherham after dismissing Michael Smith at Hillsborough on March 3 with the decision subsequently rescinded as the Millers recorded a dramatic 2-1 victory over Sheffield Wednesday.
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