Although details of the financial settlement were not disclosed, the Associated Press reports Ramone Williams received the settlement last month.
In the suit, Williams stated he was not a fan of the group and that he wandered into the bar on a whim.
Williams said he felt uneasy when the Oscar-winning group began performing the song "Let's Start A Riot."
As fans began acting out the song's lyrics, Williams stated that he was thrown to the floor, hit with a chair, stomped on and kicked in the face.
He received numerous injuries from the incident, including a fractured jaw.
Williams, who was 19 at the time of the incident, also accused the group of failing to warn the concertgoers of the violence that might occur before inciting the audience as well as failing to stop the violent behavior at the onset.
Attorneys for Three 6 Mafia tried to have the lawsuit dismissed in September, saying the group's lyrics are protected under the First Amendment of the Constitution.
Williams released Three 6 members DJ Paul (born Paul Beauregard) and Juicy J (born Jordan Houston) from the suit in April 2005, stating that the rappers were not present at the time of the assault, and thus should not be sued.
The volatile lyrics, the group claimed, were performed by Robert "Koopsta Knicca" Cooper and Darnell "Crunchy Black" Carlton, two rappers who were not regular members of Three 6 Mafia.
Williams previously won a default judgment against the club before settling with Three 6 Mafia, the AP reported.
The lawsuit was among the turbulence Three 6 Mafia endured this year.
In June, the group parted ways with Crunchy Black, who accused his former rhyme partners of putting off for years a solo album he wanted to make.