A goal three minutes from time by Dimitri Petratos was enough for the Eagles to edge out the Quake in a pulsating game to earn a spot in next weeks Grand Final against the Allstars.
In the opening exchanges both sides had chances but mainly from outside the area as both teams counter attacked fast and then sharply retracted to defend the space in front of goal.
Sydney City opened the scoring when Chris Hanly seized on a loose ball turned onto his right foot and lashed a shot from an acute angle inside the left post to give the Eagles the lead.
The Quake appeared a little destabilised after conceding the opening goal as the Eagles kept up the pressure for a second goal with committed Quake defence preventing them from going further behind.
Moments before half time the Eagles lost possession with the keeper out of goal. David Van Dinklage pounced on the loose ball and his long range shot from near his own goal line went perilously close to levelling the game.
The Quake started the second half with renewed vigour as the Eagles keeper made a fine save from Daniel Fulton.
Sydney City nearly doubled their lead as Aaron Cimitile went close when his shot crashed against the crossbar.
The Quake were desperate to level the game and applied most of the pressure with the Eagles trying to hit hard on the break.
The Quakes pressure bore results when they levelled the game through Mark Symington. A long range shot was turned around the post by the keeper and from the corner Symington stepped up unmarked and drilled his shot home to make it 1-1.
The game swept from end to end at a frenetic pace. Both sides were very combative with especially committed defence in front of goal.
Despite both sides were attacking at will but appeared that the Eagles were getting the upper hand and their possession told when they took the lead with only 3 minutes left on the clock.
Dimitri Petratos pounced on a sudden loose ball down the left side and belted a shot from a wide angle just inside the right post to seal a win for the Eagles.
The Quake went on outright attack but could not breach the Eagles solid defence. After finishing clear leaders at the top of the table the Quake bow out by the slimmest of margins.
But there was joy for the Eagles who just shaded the game on the balance of play and chances and will go on to challenge the Allstars in what should be a fabulous Youth grand final next saturday.