A 20th-minute strike by Blackburn striker Matt Derbyshire was enough to give Stuart Pearce's side the three points at Leicester's Walkers Stadium.
That maintained the England youngsters' 100% qualifying record and kept them firmly on course for the 2009 European Under-21 Championship.
Onuoha stood firm in the England defence while keeper Hart dealt easily with the little that came his way. Onuoha also went close to doubling England's lead when he headed against the crossbar just after the hour mark.
The Blues duo are set to remain in the side for Tuesday's away game against the Republic of Ireland.
Michael Johnson was also named in the squad but withdrew in order to rest a groin injury.
England: 1 Joe Hart, 2 Martin Cranie, 3 Andrew Taylor, 4 Andrew Surman (14 Fabrice Muamba, 30), 5 Steven Taylor (c), 6 Nedum Onuoha, 7 James Milner, 8 Tom Huddlestone, 9 Matt Derbyshire (17 Cameron Jerome, 79), 10 Gabriel Agbonlahor (16 Michael Kightly, 83), 11 Theo Walcott.
Subs not used: David Wheater, Ben Alnwick, Adam Johnson, Luke Moore.