The Magpies boss lost his cool on the sideline and headbutted David Meyler during his team's win on Saturday
The 52-year-old clashed with the player in his technical area during his side's 4-1 win at the KC Stadium on Saturday.
A statement from Newcastle read: "Newcastle United are disappointed with the actions of its manager Alan Pardew this afternoon.
"His behavior was unacceptable and is not the behavior we expect from the manager of Newcastle United.
"It is most disappointing that this incident has taken the focus away from what was a fantastic performance by the team and an excellent result away from home which leaves the club in eighth place in the Barclays Premier League.
"Sadly, the headlines tomorrow will not be focused on the result or the efforts of the players, but instead on the actions of our manager.
"Alan unreservedly apologized immediately following the game to the player, to Hull City Football Club and its fans, and to the fans of Newcastle United.
"We have held discussions this evening with Alan who has offered his sincere apologies to the club and it is clear he deeply regrets his actions. Alan has accepted a formal warning from the club in relation to his behavior today and also a club fine of £100,000.
"The club is now drawing a line under this matter and will be making no further comment."