Pardew still faces a separate fine from the FA and a lengthy touchline ban after being sent off for headbutting Hull City midfielder David Meyler during his side's 4-1 win at the KC Stadium on Saturday.
But Newcastle's fine, while severe, appears to end speculation that the Magpies could have used the incident as grounds for a sacking of Pardew by reason of gross misconduct - a possibility taken so seriously that one major bookmaker even suspended betting on Pardew's chances of surviving the season.
"His behaviour was unacceptable and is not the behaviour we expect from the manager of Newcastle United," the club said in a statement.
"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.
"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 behaviour 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."
Pardew was sent to the stands by referee Kevin Friend in the 72nd minute of the Premier League match for his attack on Meyler, who was booked for his part in the incident.
Pardew told Sky Sports: "I will have to sit down from now on because that's two or three incidents I've been involved in. It was a heat of the moment thing - I massively regret it.
"I didn't mean to do anything aggressive but I did move my head forward and that's enough. I wouldn't have got involved if I'd been on the other side of the line. Perhaps it will teach me to sit down.
"It's a shame because it took the gloss off a fantastic performance from us."
Ladbrokes quickly suspended betting on Pardew being the next Premier League manager to lose his job following the incident, while William Hill slashed their odds on his sacking after releasing a statement suggesting that the under-fire manager's five-year contract could be terminated for gross misconduct.
"We wait to see how Pardew's actions are dealt with," said Ladbrokes spokesman Alex Donohue.
"Keeping the market open during games often keeps us on our toes but we've never come across circumstances like this to date."
Hull manager Steve Bruce told Sky: "It was a good job it was David Meyler because we have seen people rolling around on the floor but David has acted okay.
"But I think Alan knows he has been stupid and he has apologised. We all do stupid things in the heat of the game and Alan will regret it. He has led with his head and he will regret it.
"I haven't seen anything like that before. It is an unsavoury incident but we have accepted his apology and we move on."
Newcastle were leading 3-1 when the incident occurred after goals by Moussa Sissoko and Loic Remy had put them 2-0 ahead by halftime before Curtis Davies gave the home side some hope with a header at the start of the second period.
Sissoko restored Hull's two-goal lead after 55 minutes and Vurnon Anita added the fourth in the dying minutes.
But the game was overshadowed when Meyler and Pardew clashed on the sideline after the Ireland international ran into the Magpies boss and manoeuvred him out of the way to take a quick throw in.
Pardew moved his head towards the midfielder and was promptly sent off after Meyler received his booking. Pardew stared straight at the referee, then marched off.
On the opening day of last season, Pardew shoved assistant referee Peter Kirkup and was given a two-match ban and fined £20,000 pounds by the FA for improper conduct.
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