The lawsuit, filed on Thursday in a New Orleans federal court, said Goodell "made public statements concerning Vilma which were false, defamatory and injurious to Vilma's professional and personal reputation."
NFL spokesman Greg Aiello said the league had not yet reviewed the lawsuit.
"However, our commitment to player safety and the integrity of the game is our main consideration," he said.
"We recognize that not everyone will agree with decisions that need to be made."
Vilma has been suspended by Goodell for the 2012 season for his role in the scheme that reportedly paid players thousands of dollars to injure opposing teams' top players.
But Vilma, in his lawsuit, said he had "never 'pledged,' made or received payments of any kind encouraging or resulting from an opposing player being injured."
As a result of an NFL investigation into the reported scheme, Goodell suspended former Saints defensive coordinator Gregg Williams indefinitely and head coach Sean Payton for the season.
General manager Mickey Loomis and assistant head coach Joe Vitt drew shorter suspensions as did Saints defensive end Will Smith and former Saints Anthony Hargrove and Scott Fujita.
All four players have appealed their suspensions.