Gomez went to ground after colliding with Victory's Eloise Wilson during the second half of the 1-1 draw in Saturday's Unite Round clash at Jubilee Stadium.
After receiving on-field medical attention, the 22-year-old was able to walk off the pitch slowly but needed ice on her right knee as she watched from the bench.
Peta Trimis replaced Gomez, who cut a forlorn figure as she watched on.
"Obviously we wish Gomez all the best and we pray that she's okay," Mariners coach Emily Husband told Paramount Plus.
Wilson was shown a yellow card for the contact.
Gomez's injury comes ahead of the Matildas' friendlies against Brazil, in Queensland on November 28 and December 1, and against Taiwan in Victoria on December 4 and 7.
Gomez was one of five players handed her first call-up by interim Matildas coach Tom Sermanni last Friday, and could be in doubt for her debut depending on the severity of her knee injury.
Captain Kayla Morrison salvaged a point for the Victory with a header in the final minutes of regulation time in the clash with the Mariners.
KAYLA MORRISON!!— 10 Football (@10FootballAU) @gomvfc have scored against @CCMariners with enough time still up their sleeves to win!!#UniteRound | #ALeagues | @aleaguewomen | #CCMvMVC | Live & Free on 10 Bold | https://t.co/9T25mCDGrc pic.twitter.com/dCfmf17suuNovember 23, 2024
Victory fell behind attempting to avenge last year's elimination final heartbreak, Brooke Nunn creating the opener for teenage striker Annalise Rasmussen only 12 minutes into the game.
The Melburnians did not have a shot on target until the final six minutes of regulation time but just when history looked set to repeat itself, Alana Jancevski lined up a free kick from outside the box.
She found New Zealander Claudia Bunge, who flicked the ball up for captain Morrison to head for home.
The Mariners had one final chance to snatch victory from a free kick in the last minute of added time but American import Brianne Riley could not get boot to ball as Taylor Ray crossed to her.
The Mariners will rue letting a second win of the season slip through the fingers, but nevertheless remain unbeaten through four rounds - impressive given they have faced the top four from last season's ladder in that time.
