The Stockport-born 17-year-old netted two stunning efforts to hand the away side a two-goal lead at the the Landore training ground on a wet and windy night.
Those who braved the weather witnessed a battling Blues display, as the visitors fought bravely to hold on to their lead after Oli McBurnie had halved the deficit on 64 minutes, before Gonzalez restored the two-goal cushion and sealed the win with eight minutes remaining.
Manager Simon Davies tested his young charges against what would prove to be a very experienced Swansea one.
The Welsh outfit fielded a side featuring Nathan Dyer and Leon Britton, while City had an entirely teenage starting XI with 19-year-old Tosin Adarabioyo the most senior starter.
City started brightly with Tom Dele-Bashiru creating the first clear-cut opportunity, stinging the palms of the Swansea ‘keeper inside five minutes.
The Blues broke the deadlock on 14 minutes as Foden netted a superb individual goal, turning his marker and drilling beyond Erwin Mulder.
The hosts responded well but found the away side tough to break down. Joel Latibeaudiere did well to clear, while Aro Muric also proved difficult to beat.
The Blues took their lead into the break and their second would arrive two minutes after the restart, as Foden collected a pass inside the area and smashed into the near post from a difficult angle.
Brahim Diaz was also unfortunate to see two efforts creep round the post, while Dele-Bashiru’s attempt was well-saved.
At the other end, Muric was on hand to deny McBurnie but the striker would halve the deficit, touching home Aaron Lewis’ cross shortly after the hour.
City regained their two-goal cushion however with an excellent counter-attacking move when substitute Gonzalez swept home Benjamin Garre’s delivery.
As the Swans sought a late route back into the game, Latibeaudiere cleared off the line once again and the Blues ran out 3-1 victors on an impressive night.