The suit in U.S. District Court in New Orleans claims Goodell, "relied on, at best, hearsay, circumstantial evidence and lies" in making comments about Vilma while discussing the NFL's bounty investigation of the New Orleans Saints.
Goodell has said Vilma was a leader of the team's bounty program that put up thousands of dollars for hits which took out opposing teams' star players from 2009-11, including $10,000 each on then-Arizona quarterback Kurt Warner and then-Minnesota quarterback Brett Favre during the playoffs in 2010.
"Commissioner Goodell opted to make very public and unfortunately erroneous allegations against Jonathan," said Vilma's attorney, Peter Ginsberg. "By making these false and public statements, he has significantly harmed Jonathan's reputation and ability to make a living.
"By suing Commissioner Goodell in court, Jonathan opted to use a fair playing field where he has procedural rights and protections to remedy the harm Commissioner Goodell has done to him."
Vilma wrote on his Twitter account that, "As I've said before..I NEVER PAID, NOR INTENDED TO PAY ANY AMOUNT OF MONEY, TO ANY PLAYER FOR INTENTIONALLY HURTING AN OPPONENT."
Goodell has suspended Vilma, an eight-year veteran and defensive captain, for the entire 2012 season. Vilma and three other current of former Saints who received shorter suspensions - defensive end Will Smith, defensive lineman Anthony Hargrove and linebacker Scott Fujita - all have appealed their punishments. Hargrove now plays for Green Bay while Fujita is with Cleveland.
"We have not yet reviewed the filing," NFL spokesman Greg Aiello said. "However, our commitment to player safety and the integrity of the game is our main consideration. We recognize that not everyone will agree with decisions that need to be made."
The NFL also hired former federal prosecutor Mary Jo White in late 2011 to review its evidence in the case, and White has said the NFL's findings are corroborated by multiple independent witnesses as well as documentation.
Vilma's lawsuit, which is expected to be heard by Judge Ginger Berrigan, asks for unspecified monetary damages as well as punitive damage and attorneys fees.
The lawsuit states that Goodell, "knew and intended that Vilma would suffer severe emotional distress" when the NFL published its bounty report and handed down punishment for the 30-year-old linebacker.
"Vilma will soon have to leave behind the world of professional football and will likely face difficulties in obtaining other employment and entering into new ventures as a result of Goodell's false and defamatory statements," the lawsuit said. "Media will forever mention his name in the context of the Bounty investigation and fans will forever remember Vilma with ill repute rather than remember his substantial accomplishments on and off the field."
The players' association has said that the league has refused to turn over what the union would view as hard evidence that Vilma or the other sanctioned players tried to intentionally injure targeted opponents, or sponsored such behavior.
"It is certainly the case that in court, Jonathan will have a right to see whatever it is that Commissioner Goodell has been hiding from us and what Commissioner Goodell contends gave him a basis to make these false allegations," Ginsberg said. "We will have a fair and neutral judge to preside over the dispute rather than contending with the executioner also being the person making the final decision."
Vilma's lawsuit states that the linebacker "never `pledged,' made or received payments of any kind encouraging or resulting from an opposing player being injured."
The NFL found that former Saints defensive coordinator Gregg Williams oversaw a bounty program in New Orleans from 2009 to 2011 which paid off-the-books cash bonuses of $1,500 for "knockouts," or hits which forced a player out of games, and $1,000 for "cart-offs," which left players needing help off the field.
The Saints have been punished harshly as an organization. Head coach Sean Payton has been suspended for all of 2012 for failing to put a stop to the program and attempting to cover it up, while general manager Mickey Loomis has been suspended eight games and assistant head coach Joe Vitt six games. The club also was fined $500,000 and docked two second-round draft picks.
Williams, now with St. Louis, has been suspended indefinitely.
Payton, Loomis and Williams all have issued written public apologies regarding the bounty scandal.