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Charlton slipped to a third defeat in a row on Friday night at Meadow Lane.
The result left Chris Powell's side two points outside the play-off places before Saturday's games, but with three games in hand on sixth-placed MK Dons.
Neal Bishop's bizarre 49th minute goal was enough to separate the sides, but Bradley Wright-Phillips had a tame penalty kick saved by County keeper Stuart Nelson shortly after.
Bishop's first goal of the season came just after half-time when Alan Gow's free-kick deflected off his backside and into Addicks keeper Rob Elliot's net.
Joe Anyinsah was fouled by Mike Edwards in the 63rd minute to give Charlton hope of levelling the scores, but Wright-Phillips was unable to convert the penalty, shooting straight at Nelson.
On-loan Liverpool striker Nathan Ecclestone should have put Charlton ahead before half-time, but Nelson rushed off his line to prevent him finding the net when one-on-one.
Craig Westcarr almost doubled Notts County's lead before full time. His shot from just outside the area was tipped over by Rob Elliot.