LOS ANGELES — With the season ticking away and stoppage time dwindling, LAFC did exactly what they had to do on Decision Day.

But would the Galaxy?

When a header from defender Marlon Santos found the back of the net in the 91st minute at BMO Stadium, LAFC snatched a 3-1 win and the crucial tie-breaking edge in goal differential — presuming the Galaxy went down to defeat.

Suddenly, it seemed plausible that the Black & Gold could steal away the No. 1 seed and homefield advantage from their city rival.

“For me it was incredible,” said Santos. “This group, this team deserved it and I think at the end of the match we had the reward.”

During seven minutes of stoppage time in Houston, a video review confirmed a Galaxy penalty that was ably converted by Gabriel Pec at 90+6.

LAFC coach Steve Cherundolo thought all hope was lost after Pec scored.

“I actually turned the game off,” he said. “I thought it was done and dusted.”

But as players and fans in L.A. kept tabs of the action in Texas, former Galaxy player Daniel Steres proceeded to stick a dagger in the back of his old club, delivering a header for Houston in the 101st minute that set BMO Stadium ablaze.

LAFC was already guaranteed to host two of three matches in the opening-round series for the MLS Cup playoffs. They welcome the winner of Wednesday’s play-in game between Vancouver and Portland next weekend as the journey for a third straight trip to the MLS Cup final begins.

If LAFC advances beyond the opening round they will not have to travel again unless they meet the defending league champion Columbus Crew or Inter Miami in the final.

“Save your energy,” Ilie Sanchez told the crowd after the results were set in stone. “The best is yet to come.”

For more than an hour LAFC (19-8-7) couldn’t get much right. Then the match — and the regular season — reached the last 30 minutes and the Black & Gold turned the screws on San Jose.

With the team pressuring more direct and taking risk to get in behind the Earthquakes back line, the club’s leading scorer, Denis Bouanga, bagged his 20th goal of the season.

Just the fourth MLS player to score that many times in back-to-back seasons, Bouanga’s finish 64 minutes in came after chesting down an errant clearance in the box and drilling his shot past Brazilian goalkeeper Daniel.

With 15 minutes left in regulation, Eduard Atuesta replaced Timothy Tillman in LAFC’s two-man midfield alongside Lewis O’Brien and immediately gave his club the lead with his fourth goal of the season.

“We did know as soon as you get one they’ll fall in a deeper block and windows will open and chances will come,” Cherundolo said. “I couldn’t be happier with the second half but was really disappointed with the first half performance.

“There were some words at half, for sure. Inspirational? Probably not. Emotional? Very much so.”

Facing a historically bad defensive opponent in the regular-season finale — the Earthquakes conceded a single-season record 78 goals this year — LAFC was uncharacteristically quiet in the first half.

Frustrated by LAFC’s inability to combine and dictate the terms of the match against a team that tied the record for most losses (25) in a single season on Saturday, fans at BMO Stadium let referee Pierre-Luc Lauziere know that they did not appreciate his officiating.

However by the final whistle, having fired off a season-high 11 shots on target in a single half, all was forgotten.

Struggling to combine and dictate the action despite having a nearly 60% possession rate through 45 minutes, LAFC’s lack of sharpness before the break gave San Jose (6-25-3) the break it needed to grab a 1-0 advantage.

Deep in their end of the field, defender Eddie Segura struck a pass to no one in particular. Earthquakes defender Paul Marie picked it up and dished the ball to midfielder Jackson Yueill, whose only goal of the season came from 8 yards away with his left foot in the ninth minute.

LAFC goalkeeper Hugo Lloris made four saves the rest of the way, including a massive stop in the 88th minute against the Earthquakes’ Amahl Pellegrino .