The game can be played by up to two players simultaneously, with each player controlling a different character. Before the game begins, the player chooses between the four main characters; Mike Haggar, Guy, Lucia and Dean.
Each has his or her own fighting style and attributes. Lucia is the weakest but has faster attacks, Haggar is the strongest but also the slowest, with Guy and Dean being more balanced - Guy slightly faster but weaker than Dean.
The controls consists of the d-pad and two buttons for attacking and jumping. The player character can move in any of the eight directions, but can only face and attack to the left or right like in most beat-'em-ups. Pressing both buttons simultaneously performs a special move that attacks in both directions, though uses a little health. Players can also grab and throw opponents, as well as use various weapons.
New innovations in the series include the option to have the computer AI control the second player, and the introduction of command-input "special moves" like in the Street Fighter series. Another addition is the introduction of a Super Gauge like in Super Street Fighter II Turbo, which fills as the player strikes enemies and, when full, allows the player to unleash a devastating Super Move. Also, the player can run and backdash, with character-specific special running attacks possible while running. Furthermore, the game introduces weapon specializations - each character has a weapon they're most proficient in and when they have it, they are able to use a special weapon attack in addition to the regular variation that the other characters can do when holding that weapon. Finally, the game introduced hidden areas, branching game paths and multiple endings.
Following the Mad Gear Gang's defeat in Final Fight 2, a gang war erupted in Metro City with the Skull Cross Gang eventually reigning supreme. Guy returns to Metro City following his training and meets with Mayor Haggar. The Skull Cross Gang then detonates a bomb and incites a riot in downtown Metro City, freeing their leader Marshal Black, from prison. Joined by female police officer Lucia Morgan and a mysterious street fighter named Dean, Guy and Haggar fight to take down the new gang of criminals. On the rooftop of the Skull Cross Gang's headquarters, the quartet managed to defeat and kill Black by hitting him through the electric generator, ending their crimes.
- Ray/Billy - A basic member of the Skull Cross gang that attacks with a three-hit combo punch.
- Dirk/Rick - A typically weak punk from the Skull Cross gang. However, this particular member has metal claws similar to those of Marvel Comics superhero Wolverine.
- Fat Jack/Arby - Football player-style Skull Cross member who comes running from one side of the screen to the other like a juggernaut.
- Hunter - A tall man that wears a hockey mask and baseball cap and walks in a hunched over, shuffling gait. He boasts a basic punch attack as well as a slide attack, but his most powerful attack is a slow, powerful swing from the baseball bat he keeps strapped to his back which can take out almost all of the player's health in a single strike.
- May - Female ninja-like Skull Cross member who slices with a kunai attached at her wrist. She will backflip out of harm's way when attacked.
- Fritz - Another one of those classic Final Fight punks that run by, tossing molotov cocktails and leaving a fiery mess in their wake.
- Dave - A renegade cop who has crossed over to the Skull Cross gang. Wielding a billy club, his deadliest attack is the Giant Jump. He is similar in appearance to Edi E. He was defeated by Lucia.
- Callman - The head waiter of "Creep Eats", a barbecue joint located in the back streets of Metro City. He was defeated by Lucia.
- Drake - This mad fisherman, dressed in a blue tanktop, blue jeans, a blue sailor hat and brown boots, attacks with a big anchor. He is in charge of the gang's cargo ship which contains weaponry smuggled via Sims Inc. He was defeated by Dean.
- Caine - The gang's mechanic. Caine attacks the player with a gigantic wrench in an abandoned bus yard, but this large boss is nearsighted and slow-moving. He was defeated by Guy.
- Wong - This boss has a long ponytail with no other hair on his head. Wears a green cloth, brown shorts, brown boots, silver wrist guards, a brown strap to hold his top, and has a set of beads on his hand. He was defeated by Guy.
- Stray - Stray, the penultimate boss of the game, moves fast, jumping and striking with lightning speed. Armed with spiked knuckles, Stray wears a green trenchcoat with purple pants, gloves and has a spiky mohawk. He was responsible for the slaughter of Dean's family. Dean defeated and killed him.
- Black - Black is the leader of the Skull Cross Gang and the final boss of the game. He uses a flogging whip as his main weapon, occasionally throws knives, and possesses a spinning attack that is similar to Haggar's "Lariat", and a ki attack similar to Guy's "Palm Blast Attack". Black has a strong resemblance to Fist of the North Star villain, The Colonel, with his clothes, red beret, scars and eyepatch, and borrows his jacket bursting action from the series main protagonist, Kenshiro.
Final Fight 3 consists of six stages or "rounds", as well as two bonus rounds. Each round takes place in a different locality in Metro City, with most rounds featuring more than one level. At the end of each round the player will face a boss character unique to that round.
The game possesses a branching path system wherein the player will take a different route through the game depending on the fulfillment of certain criteria - entire boss battles can be skipped by taking alternate exits and most significantly, Round 4 will take place in one of two different locations (with different bosses) depending on whether the player took the bus in Round 3 or not.
- This was the first Final Fight game to feature four playable characters.
- In the European version of the game, holding Select until the Capcom logo fades away will bring up a debug menu which allows for various cheats such as health regeneration and a stage select. In the North American version of the game, this is disabled and only accessible via an Action Replay or similar device.
Unlike the series' previous entries, the game lacks a credits sequence for the game's staff.