Nico O'Reilly had put City ahead in the first half, after finishing off a fine move with a superb finish.
But two goals in nine second half minutes from Vasco Walz and Julian Rijkoff turned the game in Dortmund's favour, with less than 10 minutes remaining.
However, City rallied late on, scoring twice in the dying embers of the game, to make it two wins from two in Group G.
The beginning of the match was tightly contested, with both teams testing each other’s resolve in defence.
Dortmund gave our high defensive line a fright early on, as Kane Taylor misjudged the bounce of the ball, which set Samuel Bamba free, but he could only fire his shot into row z.
Our Young Outfit responded effectively, as Shea Charles cut open the visitors back line with a pass to Oscar Bobb, who forced a save from Marian Kirsch.
City were unfortunate not to be ahead after we did well to press the visitors into gifting us possession, and it landed to the feet of Charles, who repeatedly threaded a ball through the back line and Nico O’Reilly took too long with his shot, as Kirsch flew out to deny him.
But despite both teams having chances to score, it was advantage City just after the half hour mark.
Carlos Borges did well to keep the ball in play on the left before he slide a cross into Nico O’Reilly, who did not miss this attempt, as the number 10 curled the ball away from the goalkeeper to put us ahead.
Half chances were missed as the first half closed with City ahead.
The second half started with a much higher tempo with both teams crafting opportunities in the first few minutes.
The Black and Yellow’s substitute, Noa-Gabriel Simic did well to open up space but to our fortune, his finessed shot met the gloves of Mikki Van Sas.
Moments later down the other end, Borges was played through in behind Dortmund’s defence and his chip looped just over the crossbar to the winger's frustration.
But it was the visitors who were on the ascendancy, as they searched for the equaliser.
And they were not too far away, as Lion Semic drove into the box and his cross clipped Tom Galvez, and bounced narrowly out for a corner.
The German Outfit eventually made their second half dominance count, as Dortmund pressed well from our goal kick, and Simic passed the ball low across to Vasco Walz, who’s effort met the glove of Van Sas, but flew into the net.
Not long after, Julian Rijkhoff was adjudged to being fouled in the box and the following penalty was converted confidently by their number nine to turn the game around.
But the action was not over yet, as City were awarded the second penalty of the match late on, which Bobb converted to draw us level.
With four minutes of added time being announced around the Academy Stadium, City were gifted with renewed hope of victory, as Barry-Murphy's Young Charges pushed for a winner, and this proved to be our future.
Substitute Joel Ndala did well to latch onto a chance in the box, with his first chance saved, he reacted athletically to twist, shoot and ripple the net to give City a second win of the group stages.
HOW WE LINED UP
Brian Barry-Murphy stook with his trusted 4-3-3 formation, with Mikki Van Sas starting between the sticks.
He was protected by a back four of Lakyle Samuel, Finley Burns, Kane Taylor and Tom Galvez.
Shea Charles sat just in front of them with Oscar Bobb and Nico O’Reilly further ahead in the engine room.
Will Dickson played as a sole striker with Dire Mebude and Carlos Borges playing on the flanks.
Starting XI: Van Sas, Samuel, Burns (85’ Alleyne), Taylor, O’Reilly, Charles, Bobb, Mebude (78’ Ndala), Dickson (79’ Adam), Borges
SUBS: Murray-Jones, Wright, Oboavwoduo, Whittingham
Starting XI: Kirsch, Collins, Cisse, Walz, Rijkhoff (86’ Lubach), Bamba (46’ Simic), Aning, Gürpüz (69’ Ludwig), Josua Brunner (90’ Rashidi), Semic, Mane
SUBS: Zacharias, Korzynietz, König
WHAT IT MEANS
City have a 100% start to our UEFA Youth League Group G campaign.
It's now six points from six for Barry-Murphy's men.
Our EDS are back playing Premier League 2 football this weekend when we host Fulham at the Academy Stadium.
Kick-off is scheduled for 14:00 (UK).
And our next UEFA Youth League assignment sees us take on FC Copenhagen at home on Wednesday 5 October at 15:00 (UK).
News about Man City v BVB
Ticket details: City Under-19s v Borussia Dortmund
Essential ticket information ahead of City's UEFA Youth League game with Borussia Dortmund on Wednesday, September 14 at the Academy Stadium. Read more
Watch City Under-19s v Borussia Dortmund live on CITY+ and Recast
Manchester City’s Under-19s continue our UEFA Youth League campaign on Wednesday when we play host to Borussia Dortmund, with all the action available to follow live on CITY+ and Recast. Read more