It is the second trophy won by the Crew under French coach Wilfried Nancy following the team's MLS Cup triumph - also over LAFC - last December at their Lower.com stadium.
The Crew, who also reached the final of the CONCACAF Champions Cup, losing to Mexico's Pachuca in June, have won admirers in North America for their attractive and progressive football.
The finishing ability of Hernandez, a forward who had spells in England and Spain, was once again crucial for Columbus.
Hernandez put the Crew ahead on the stroke of half-time with a powerful header after a clever chip into the box from Mohamed Farsi.
Former France and Arsenal striker Olivier Giroud, making his first start for LAFC following his recent move from AC Milan, levelled in the 57th minute with a trademark header from a Mateusz Bogusz corner.
The goal brought LAFC to life and they enjoyed a spell of strong pressure with the Crew back-line struggling to cope.
With the game heading to penalties, Hernandez floated in a hopeful ball from the inside-left position that passed across the area and the unsighted LAFC goalkeeper Hugo Lloris was unable to keep it out.
Hernandez celebrated by removing his shirt and jumping into the crowd but he preserved enough energy to make another decisive contribution.
The Colombian created the third, leading a counter-attack deep in stoppage time, breaking away before slipping the ball to substitute Jacen Russell-Rowe, who coolly slotted home.
“I have no words, I continue to make history in this club," said Hernandez.
"This is my work. Good work brings reward and this is the reward. The mentality that this team has is rarely seen in other teams," he said.
Nancy said his team had shown their qualities once again.
"It's amazing. This is again the possibility to show that we are consistent, to show that we are good, to show that we are able to face adversity," Nancy told Apple TV after the game.
"Yes, we play the way we play, but at the end of the day, this is (about) the spirit. This is the most important thing, to do it in front of our fans. Memories, the memories are going to be amazing," he added.
The loss was the latest disappointment for Steve Cherundolo's LAFC, who since winning the MLS Cup in 2022 have lost in the CONCACAF Champions Cup final to Leon before their two defeats in the finals to the Crew.
Both the Crew and LAFC qualified for next year's CONCACAF competition along with the Colorado Rapids - who finished third in the Leagues Cup after beating the Philadelphia Union on penalties.
