City lost superstar striker Holly McNamara to concussion in the 10th minute and were reduced to 10 players just 15 minutes later when Lourdes Bosch needlessly hit Mariners forward Brooke Nunn in the face and received a straight red card.
The Mariners finally made the most of their numbers advantage in the 121st minute 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 offside.
The Mariners - the only team not to lose to City this season - progress to the grand final 3-2 on aggregate after first fighting out a 2-2 draw in their home leg.
They will face Victory, who beat Adelaide 6-2 on aggregate, at AAMI Park next Saturday.
City's hopes of a treble are now over and they will soon travel to China to take on South Korea's Incheon Red Angels in their Asian Champions League semi-final.
The game was turned on its head when McNamara was injured.
McNamara was showing dangerous form but her match came to an early end in the 10th minute when she went up for a header against Mariners goalkeeper Sarah Langman and the pair heavily clashed heads.
Both hit the deck, with McNamara staying down requiring treatment.
The distraught striker slowly walked off the field and was quickly ruled out of the game, with Shelby McMahon replacing her.
McNamara would have been unable to play in the grand final due to concussion protocols and City will hope she recovers well enough to feature in their Champions League campaign.
The 22-year-old has had an extraordinary season, scoring 15 goals in 18 games after returning from her third career knee reconstruction.
Sunday's game could also have been her final ALW appearance, as McNamara has attracted attention from overseas.
Both teams had chances to win the game in regular and added time before Trimis teed up Gomez for the winner.
