City's man-of-the-match was keeper, Kevin Ellegaard, who made a number of quality saves to frustrate the visitors. However, the Magpies scored the only goal of the game through Michael Chopra, two minutes after the restart.
City might have drawn level through Stephen Elliott but the young striker didn't have his shooting boots on. He missed chances in both halves, coming closest with one effort cleared off the line.
Paul Murphy headed a corner goalwards but was also denied on the line while City had a late penalty shout refused.
Subs Carlos Logan and Stephen Ireland added fresh impetus for City but were unable to help the Blues to the draw which they probably deserved.
City have now won only once and lost three of their first six games. They meet Bolton in a Manchester Senior Cup tie at Lancashire County FA's headquarters at Leyland next Wednesday.
Meanwhile, the U17s Youth Academy side play Leeds at Thorp Arch on Saturday, while the U19s meet Derby County - both kick-off at 11am.
City: Ellegaard, Warrender, Collins, Murphy, Bischoff, Jordan, Bennett (Logan 74), Whelan, Berkovic (Ireland h-t), Elliott, B. Wright-Phillips.
Subs not used: Schmeichel, Lee-Matthews, Smith