The Hobbit pub has been accused of copyright infringement by lawyers representing the Saul Zaentz Company (SZC) in California.
Mr Fry, in New Zealand working on the forthcoming film of the Hobbit, called it "pointless, self-defeating bullying".
His support boosted the pub's Facebook supporters to more than 15,000.
SZC owns the worldwide rights to several brands associated with author JRR Tolkien, including The Hobbit and The Lord of The Rings.
The pub in Bevois Valley, which is popular with students, has traded with the name for more than 20 years.
It features characters from Tolkien's stories on its signs, has "Frodo" and "Gandalf" cocktails on the menu, and the face of Lord of the Rings film star Elijah Wood on its loyalty card.
The Lord of The Rings films and the soon to be released adaptation of The Hobbit, made by New Line Cinema, have been licensed from SZC.
A letter from SZC asked the pub to remove all references to the characters.
The company asserts it has "exclusive worldwide rights to motion picture, merchandising, stage and other rights in certain literary works of JRR Tolkien including The Lord of the Rings and The Hobbit".
Writing on Twitter, Mr Fry said: "Honestly, sometimes I'm ashamed of the business I'm in. What pointless, self-defeating bullying."
Landlady Stella Mary Roberts said: "We are overwhelmed. The support has been phenomenal.
"At the end of the day it is a legal matter. This just shows people's support and how petty the actions of the lawyers are."
She added there was a "flood" of customers wanting to buy Hobbit T-shirts when the pub opened on Tuesday evening.
Also on Twitter, MP for Southampton Itchen John Denham said: "You would have thought the film company makes enough money to be able to leave the popular Hobbit pub in Southampton alone."
Michael Coyle, intellectual property expert from Lawdit Solicitors in Southampton, said: "The problem for Stella is these guys have so much money and costs could run into six figures. It's a game of poker - ultimately they would win because they have deeper pockets.
"It would be difficult to stop the pub from using the name - it would be very unfair because of the length of time they have used it. Where perhaps the problem would lie is in using images, photographs and the names of drinks.
"But it's not going to do the film's PR any good - all the sympathy is with the pub so it will have a backlash as well."
Punch Taverns, which owns the freehold to the building, said: "We are aware of the situation and are currently consulting with our legal advisers."
Actor Stephen Fry has backed a Southampton pub after it was threatened with legal action by US movie lawyers.