Former City youngster Luca Barrington scored an early penalty to give the Seagulls the lead heading into the half-time break.
But a lovely finish from Alex Robertson drew us level before Borges rounded off a great move to seal the win and secure all three points for Brian Barry-Murphy's side.
It wasn't an ideal start for City as a quick breakaway from Brighton ended in Tom Galvez fouling Barrington, seeing the away side awarded a penalty.
Brighton's number ten then subsequently stepped up, sent keeper Mikki van Sas the wrong way to give the Seagulls the lead with under ten minutes played.
The early goal was not undeserved for the visitors, who continued to apply pressure to our backline.
Wingers Cameron Peupion and Marcus Ifill saw efforts flash wide, as the south coast side proved to be a real menace on the break.
But, as the half wore on, the game opened up and City were able to start creating opportunities.
Borges shot wide of the far post before Oscar Bobb forced a great save from Toby Bull.
The Brighton stopper was called into action again to prevent Dire Mebude from scoring at close range before palming away an effort from right-back Lakyle Samuel.
Into the second half, we started much brighter than we did the first, immediately putting pressure on the Seagull's defence.
Borges and Robertson saw efforts flash wide of Bull's goal before we finally managed to breach the Brighton defence.
Just before the hour mark, Robertson was found on the edge of the area and the midfielder stroked the ball home with a finely taken finish, notching up his third goal in two games.
We kept flying forward in search of a winner, but the visitors were proving to be stubborn customers, and it looked as though we would have to settle for a point.
But, with just eight minutes left, a well-worked move down the right from City saw the ball flash past the outstretched arm of Bull and into the path of Borges, who made no mistake in finishing into an empty net to clinch victory.
HOW WE LINED UP
Barry-Murphy shuffled his pack against Brighton but elected to keep van Sas in between the sticks.
Lakyle Samuel and Jadel Katongo also kept their places in the back line from the Arsenal win, with Shea Charles and Galvez coming into the defence.
Robertson and Kian Breckin made up the sitting midfield two, behind Bobb in the number ten role.
Mebude and Borges lined up on the wings with Will Dickson through the middle.
Manchester City EDS
Starting XI | van Sas, Samuel, Charles, Katongo (72' Simpson-Pusey), Galvez, Breckin, Mebude, Robertson, Dickson (Adam 46'), Bobb, Borges.
Substitutes | McNamara, Smith.
Brighton and Hove Albion U21
Starting XI | Bull, Nilsson, Samuels, Offiah, Jackson, Hinshelwood, Peupion, Chouchane, Moran, Barrington (68' Everitt), Ifill
Substitutes | Talley, Wilson, Baker-Boaitey, Kavanagh.
WHAT IT MEANS
The win sees us go back to the top of the Premier League 2.
We sit one point above second-placed Chelsea having played a game less than the London side.
The next challenge on the calendar for Barry Murphy's side is an away clash against Leicester in the PL2 on Friday.
Kick-off against the Foxes will be at 19:00 GMT on Friday, 20 January.
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