The penalty Friday was the 14th the league has announced against Cuban, who has been penalized about $1.5 million over the years and suspended from three games.
Cuban went onto the court at halftime to complain to the Nuggets' J.R. Smith about an elbow he saw the Nuggets player throw.
Cuban was then angered at the end after a disputed foul called on Jason Terry led to the go-ahead free throws by Chauncey Billups with 2.2 seconds left.
Cuban didn't respond to an e-mail request for comment by the Associated Press, but wrote about the fine under an item titled "Me and JR Smith" on his blog.
After beginning the letter by apologizing to Smith for not accepting his offer of a signed pair of sneakers, Cuban continued: "The NBA tells me a tech should have been called on you for throwing the elbow and that I should pay a 25k dollar fine because owners aren't supposed to get mad. Ever.
"In the spirit of the joy of my getting fined and your not getting the tech, have the Nuggets PR folks contact the Mavs PR folks and I will donate 25k to the charity of your choice.
"Unless of course your coach thinks that the wrong thing to do, or the NBA says I can't because it would be a violation of a rule. In which case, I will find a charity that I think you would like and make the donation in your name."