The Wales captain had been named on the bench for the game after recovering from a leg injury.
He came on in the 97th minute before heading in to make it 3-3 right at the death, minutes after Philadelphia had scored.
LAFC then won the shootout 3-0 to win the title for the first time.
“It’s always nice to score in finals, and I seem to have a knack for doing that,” said Bale. “It’s big. It’s important for the club. It’s important for the fans.”
Bale’s return to fitness and his significant contribution to the win comes at a good time for Wales, who name their World Cup squad on Wednesday before the tournament in Qatar starts on 20 November.
In what was arguably one of the most memorable games in Major League Soccer history, LAFC had taken the lead in the first half when Kellyn Acosta struck with a deflected free-kick.
Daniel Gazdag equalised midway through the second half when he stopped a low shot from distance to fire in from close range.
Jesus Murillo thought he had won it normal time for LAFC with a strike in the 83rd minute but Jack Elliott equalised two minutes later.
The drama continued in extra time as LAFC had goalkeeper Maxime Crepeau sent off for a foul, which also resulted in him needing to be taken off on a stretcher.
Elliott then scored four minutes into added time in extra time and looked to have sealed it for Philadelphia.
But, with nine minutes of added time being played, Bale’s dramatic 128th-minute equaliser took the game to penalties, where substitute goalkeeper John McCarthy made two crucial saves before Ilie Sanchez scored the decisive spot-kick to seal a memorable win for LAFC.
“The reason why I came here was to try and help the club win the MLS Cup,” said Bale.
“You can see how happy everybody is now, the fans, the city. It’s important for this club to go to the next level, and I think by winning this trophy, it shows that we are.
“It’s a club really on the rise doing the right things and it’s an important trophy for us, especially the first one, first major trophy, and hopefully there’s more to come in the future.”
LAFC head coach Steve Cherundolo said Bale’s equaliser was “Gareth being Gareth”.
“He’s done it in training, he’s done it in the season,” he said. “When he’s feeling well and healthy he makes a difference in games.
“That’s why we bring him in for those moments. I wish he was 24.”