The gameplay style is revamped, replacing the engine of Shinobi Chronicles with a new 3D battle engine. Characters now have much more stamina in their health meters, which are indicated by a green gauge above their portrait. The amount of health "gauges" are determined by small orbs above the gauge. 1-5 orbs will indicate how many gauges of health are present, and a red flashing gauge with no orb indicates that the character is down to their last bit of health. There are also two energy gauges: one that is within the same HUD as the character's vitality and a numbered gauge that appears beside it. The numbered gauge is the Ultimate Meter. Ultimate Moves can only be activated once the gauge is full and displays a number from 1-4. The other gauge is the Soul Meter, which can be charged at any time and allows characters to transform or use their Special Moves, similar to Namco Bandai's Dragon Ball Z: Budokai Tenkaichi series.
Characters will fight in large, destructible 3D environments. Each character is given four special moves and an Ultimate Move. Special moves range from simple techniques, such as Rig's Ice Wolves, to cutscene-styled combos, such as Lee Hatake's "Bring the Rain" tactic. Ultimate Moves refer to cinematic or destructive techniques as in the case of Nero's Nexus Crash and Fallen Lee's Infernal Vortex. In addition, characters are no longer limited to the previous Awakening system from Shinobi Chronicles, as most characters can now awaken at any time. Regular awakenings, such as Natsuki Uchiyama's Lightning Aura and Golden Nero, can be accessed and canceled at any time, through the cost of Soul Meter energy. Other Awakenings, such as Jon's Demon Hachi form, are temporary as they will consume the energy from the character's Ultimate Meter rather than their Soul Meter. Power Struggles make their return in this game.
Revamping the Support character system from Shinobi Chronicles, players are now able to select teams of up to five characters. As with the first game, these characters are divided into Battle-Types and Support-Types. Each battle may only have one Support-Type and up to four Battle-Types. Players will have the option to switch out two of their Battle-Types at anytime, and the other Battle-Types will only be accessable by the CPU or a second player when playing multi-player battles.
Whenever certain team combinations are made, such as the Crescent brothers or any two members of Team Hatake, players are given access to Team Ultimate Moves or Team Special Moves. A Team Ultimate Move, as the name suggests, is activated whenever teammates activate their Ultimate and successfully pull off the on-screen display for a Support gauge. One such example of a Team Ultimate is "The True Chosen One", which may only be activated whenever an opponent's health is lower than one gauge and both Lee Hatake and Fallen Lee are on the same team. The resulting technique will be cinematic. A Team Special Move is activated under similar conditions, only the character merely needs to activate one of their Specials.
Concerning stage destruction, there are two forms. One form is accessed through desctructive attacks, such as Jon's Raikiri Tensho. This type of destruction will leave noticeable scars in the landscape of a stage and may destroy buildings, but are not nearly powerful enough to destroy the stage itself. This is where the second types comes in. The second destruction level is complete stage destruction. For example, if an Ultimate Move is powerful enough. it has the potential to leave entire stages ravaged and barren. Some stages have unique levels of destruction, whereas others only result in a generic wasteland.
Quick-time event boss battles are introduced, as well as introduction dialogue. For example, at the start of a battle, the camera will pan across the stage before cutting to the characters. The characters will say a line of dialogue to each other in a brief cutscene and the battle will commence. Certain characters, such as Jon Kurosaki and Draco Tenshi, will have special dialogue with each other, referencing the connection between them. In team battles, both of the primary Battle characters will say a line of dialogue to each other or their opponents, while the Support and secondary Battle characters will stand silent in the background. In additon, matching certain characters against each other in Free Battle mode will have in-game dialogue. One example is a match between Jenova Crescent and Raizo Uchidama. While fighting in-game, they will recite their famous quotes from their battle with each other.
- Shinobi Reborn was originally planned to be the first installment in the series, with Brawl Legends: Shinobi Chronicles being its handheld counterpart. This was later changed to avoid confusion in regard to the titles.