Mortal Kombat 3 brings new elements to the 2D fighting series: multi-level playfields, "Dial-A-Combo" attacks, a "Run" button to speed up the battles, and "Vs." codes, which unlock new powers and abilities once both players enter a code sequence in pre-match-up screens. Also included are more stage fatalities and finishing moves as each warrior attempts to go one-on-one with the Centaurian enforcer Motaro, and Shao Kahn himself.

Mortal Kombat 3 is the last traditional one-on-one fighting game game in the series to feature motion-captured digitized graphics for its kombatants.