Hughes was sent to the stands in his side's 5-1 Premier League loss at St James' Park on Boxing Day.
The Welshman has avoided a touchline ban and is free to take control of his side in Saturday's FA Cup third-round tie with Leicester.
A statement from the Football Association read: "Stoke City manager Mark Hughes has been fined the standard penalty of £8,000 after he admitted an FA misconduct charge.
"The charge was that his behaviour in or around the 40th minute of Stoke's game against Newcastle United on December 26, 2013 amounted to improper conduct."
Hughes was ordered from the dugout after he reacted in fury to the dismissal of midfielder Glenn Whelan, and he was still making his way to his new vantage point when defender Marc Wilson was also red-carded as the visitors endured three dreadful first-half minutes when leading 1-0.
Whelan picked up two yellow cards, the first for kicking the ball away and clashing with Yohan Cabaye after being penalised for a foul on Moussa Sissoko, and the second for a foul on Cabaye.
Wilson followed for hauling down Loic Remy inside the box, and although goalkeeper Thomas Sorensen saved the resulting spot-kick, the writing was on the wall for the numerically-disadvantaged Potters.
Following the match Hughes criticised referee Martin Atkinson, but he avoided censure for his comments.
He said: "From one of our arguably most senior referees, I was absolutely dismayed by his performance."