A headed goal by Traralgon City's Tom Sawyer in the 93rd minute of Sunday's elimination final clinched his side a semi-final showdown next Sunday against league leader Falcons 2000.
The goal broke the deadlock as Trafalgar Victory and City were tied at 2-2 with the game going into extra time.
Referee Jasmine Stega oversaw a torrid clash and had to hand out a couple of yellow cards to quell some hot-heads from both sides.
The Roosters drew first blood through a converted penalty from Liam Johnson.
Trafalgar scored the equaliser six minutes later when Anthony Sossa beat the keeper.
A goal shortly after by City's Tom Sawyer was disallowed after the offside flag was hoisted.
Trafalgar got the vital breakthrough just before half-time when Josh Paredes converted to give Trafalgar a 2-1 lead.
Victory thought it was in the box seat when a Paredes-Sossa combination went to the net but the offside flag was held up again.
Liam Johnson was hot in the middle for the Roosters and scored their second goal to level scores at 2-2.
Tom Sawyer's header in injury time changed the game to see Traralgon City take the final 3-2.
Reserves: Monash 5 d Churchill 0
Women: Trafalgar 3 d NY 0
Second division: Monash 1 d Sale 0
Newborough/Yallourn v Monash
Newborough/Yallourn has earned a semi-final berth after a 3-1 victory over crosstown rival Monash.
United got the break at the 15-minute mark when Andrew Batt belted a boomer past the keeper.
There was pressure from both sides but Monash was able to crack the Newborough/Yallourn defence with a goal through Ethan Lawrence.
Dylan Fairbrother found space on the rebound and hammered one through to give United a 2-1 lead.
New/Yall was afforded a break late in the final term when Alex Bowman scored to give his side its third goal and the win.
Reserves: Falcons 4 d NYU 1
Women: Falcons 7 d Monash 0
Second division: Fortuna 4 d Traralgon City 0
The winner of this weekend's preliminary final between Falcons and Newborough/Yallourn will move through to the grand final on 24 September.
The sides met twice during the regular season with Falcons taking the win 3-0 in the first round and the second resulting in a 1-1 draw.
Reserves: Falcons v Traralgon City
Women: Falcons v Traralgon City
Second division: Olympians v Fortuna
Olympians v Traralgon City
Traralgon City has enjoyed a stellar season after it took out the league championships in both the reserves and the women's competitions.
City now faces rivals Olympians in the local derby.
Traralgon City clinched the win in their first encounter 2-4, but Olympians turned it around in their second meeting to take a 4-1 victory.
Reserves: Monash v Olympians
Women: Fortuna v Trafalgar
Second division: Pegasus v Monash
State League 4 South
Pegasus women's team finished the regular season on a high with a massive 16-0 win over bottom side Sandringham.
Led by goal ace Holly Mccullagh with seven, the Pegs added a further ten second half goals to reach 16. Bianca Tombra scored four, Calista Lazaris two and Ayen Anyieth, Zanna Sharmeen and Chloe Rodda scored one each.