Isabel Gomez was clearly offside when she scored the winner in the 121st minute, when the Mariners finally capitalised after more than 100 minutes of playing time with an extra player.
The Mariners - the only team not to lose to City this season - progress to the grand final against Melbourne Victory, having won 3-2 on aggregate after a 2-2 draw in their home leg.
City's hopes of a treble are in pieces after a game where everything that could go wrong, did.
City lost superstar striker Holly McNamara to concussion after a head clash with Mariners goalkeeper Sarah Langman in the 10th minute.
They were reduced to 10 players just 15 minutes later when Lourdes Bosch received a straight red card.
The Mariners finally made the most of their numbers advantage when Peta Trimis capitalised on a mix-up at the back and worked the ball to Mariners superstar Gomez, who chipped Malena Mieres for the winner.
Controversy erupted after the goal, with Gomez appearing to have been at least a metre offside.
"I'm gonna be honest with you, I knew it was offside," Mariners coach Emily Husband said.
"But the flag didn't go up and that's football.
"Melbourne City were fantastic tonight. You've got to give them credit, because they made the job so, so hard for us."
City coach Michael Matricciani said: "Of course it's offside. I could see from the dugout, 45 metres away on a 45-degree angle.
"But these things happen. Everyone makes mistakes. We're all humans.
"We don't have VAR in this competition and unfortunately we copped it in the 120th minute. It happens. It's hard to take, but I'm super proud of the girls."
Central Coast face a tough task against Victory, who beat Adelaide 6-2 on aggregate.
"We know that we have the ability to overcome them," Husband said.
The game was turned on its head when McNamara was injured in the 10th minute.
The distraught striker, who has a broken nose and concussion, slowly walked off the field and was quickly ruled out of the game, with Shelby McMahon replacing her.
Next Sunday, City will travel to China to take on South Korea's Incheon Red Angels in their Asian Champions League semi-final and will hope McNamara is fit to join them.
The 22-year-old has had an extraordinary season, scoring 15 goals in 18 games after returning from her third knee reconstruction.
Bosch was sent off after she needlessly hit Mariners forward Brooke Nunn in the face.
"She's let the team down. She'll be the first to put her hand up and admit that," Matricciani said.
"It's not acceptable, it's as simple as that."
Both teams had chances to win the game in regular and added time, before Trimis teed up Gomez for the winner.
On full-time, Mariners forward Nunn sprinted along the touchline shushing City fans, and incensing Matricciani.
"For me, the biggest thing is that you need to win with a bit of respect and grace, and I don't think she showed that," Matricciani said.
Husband said of Nunn: "Look, at the end of the day players, when they're faced with adversity, they'll act out in different ways.
"We've spoken to Brooke. She's a character ... for her, it was about enjoying the moment."
