The Austrian midfield struck in the dying minutes to seal the win for the young Blues after Kyle Lafferty had cancelled out Rodney Kongolo’s 53rd minute opener.
Simon Davies made three changes to the side that beat Manchester United at the Etihad in the previous game with Tosin Adarabioyo, Brandon Barker and David Faupala coming in for Ellis Plummer, Ashley Smith-Brown and Aaron Nemane.
The first half was a cagey affair with neither side creating many noteworthy chances as both sides looked to get a foothold on the game.
Tony Andreu came closest for the home side as his shot beat Angus Gunn in the City goal before seeing his effort rattle the crossbar.
The young Blues started well after the restart and took the lead in the 53rd minute through Kongolo. Bytyqi swung a corner to the back post and the Dutch midfielder was on hand to apply the finish to give City a one-goal advantage.
However, the lead didn’t last long as the hosts pulled level within seven minutes. Andreu flicked onto Northern Ireland international Lafferty, who fired into the back of the net from close range to make it 1-1.
Both teams looked to get a winner as the clocked ticked to the final whistle and it was City who managed to find one in the dying minutes.
Barker was brought down in the box and Bytyqi stepped up from 12 yards to secure the three points and strengthen City’s hold on third place, as well as closing the gap on the top two.