The Crew added the title to their championships in 2008, when they beat the New York Red Bulls, and 2020, when they defeated the Seattle Sounders. Columbus lost to the Portland Timbers in the 2015 title game.
Only the LA Galaxy (five) and D.C. United (four) have won more titles.
Los Angeles was looking to become the fourth MLS team to win consecutive titles.
Hernandez scored in the 33rd minute and Yeboah added a goal in the 37th. Denis Bouanga scored for LAFC in the 74th.
Hernandez put Columbus up 1-0 on a penalty kick. He deposited the ball in the lower left corner for his fifth goal in six playoff matches this season. He is 9 for 9 from the spot in all competitions in his Crew career.
LAFC defender Diego Palacios was whistled for a handball off his right arm at the top of the box, setting up the penalty.
The goal was the first allowed by LAFC in four matches.
Yeboah doubled the lead when the Crew, the highest-scoring team in MLS in the regular season, when Malte Amundsen threaded a pass through to Yeboah on the left flank on the last of 11 passes in the build-up.
From there, Yeboah dribbled to the goal box and slipped a shot past goalkeeper Maxime Crepeau.
Columbus had 68.2% of the possession and led 5-1 in corners in the first half.
The objective for the Crew in the second half was to avoid the same fate as FC Cincinnati a week earlier in the Eastern Conference final. Then, Columbus rallied from a two-goal deficit in the final 15 minutes of regulation and won 3-2 in extra time.
Bouanga made it 2-1, scoring on his own rebound after Patrick Schulte made the save at the left post. Bouanga, who led the MLS with 20 goals, has 38 goals in 49 matches in all competitions this year.
The Crew missed the playoffs the past two seasons before hiring coach Wilfried Nancy from CF Montreal.