Hull drew 0-0 with fellow strugglers Portsmouth in Saturday's Premier League match at the KC stadium, which kicked off at 3pm.
"Jozy was on the bench until 2.10 when I decided to change it," said Brown. "It's unacceptable behaviour, full stop.
"You prepare all week for a match day, mentally and physically. To ask a player to arrive an hour and a half before a game is not too much to ask is it?"
Altidore is not the only sportsman to have fallen foul of his bosses for using the social networking site Twitter in recent months.
Darren Bent was forced to apologise for an online Twitter rant against Tottenham chairman Daniel Levy as he negotiated a move to Sunderland in July.
In August, tennis players at the US Open were warned against writing updates on Twitter during matches for fear it could violate anti-corruption rules.
While batsmen Phillip Hughes caused red faces at Cricket Australia when he tweeted that he had been dropped from the third Ashes Test before it had been officially announced.
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