Two goals by Mark Stallard earned County a shock victory and dealt a severe blow to the Bluebirds automatic promotion hopes.
He netted a 61st minute penalty and then sealed an unlikely victory ten minutes from time.
"My immediate reaction in the dug out was that it wasn't a penalty and on seeing it again it looked as though any contact was outside the box," said Bluebird's boss Lennie Lawrence.
"But we didn't do well enough at either end of the field. And we have got to put things right, particularly at home." Cardiff now have only won one of their last six games at Ninian Park and have now moved closer to the play-offs where they had such heartbreak last season.
City looked to spring heeled leading scorer Robert Earnshaw to open up the visitors defence but it was skipper Graham Kavanagh who almost opened the scoring when his floated cross beat keeper Steve Mildenhall only to drift wide of the far post.
Minutes after the inetrval the visitors almost took the lead when a loose clearance from City went straight to County skipper Ian Richardson and his first-time volley was brilliantly tipped over by Bluebird's keeper Neil Alexander.
With 60 minutes gone Paul Heffernan tumbled in the box and referee Lee Cable signalled a penalty and Stallard slotted the spot kick into the corner of the net to give the visitors the lead.
Stallard the n wated a golden opportunity to extend the Magpies’ lead, but he was not to be denied with ten minutes remaining when he took advantage of slack marking in the City penalty area to crash a shot into the corner of the net.
County manager Billy Dearden was very pleased with his side's performance.
"We did well particularly in the second half,†he said. “Away from home this is probably our best performance all season.
“It is never easy coming to Cardiff but we thought we could get something from the game as we knew about Cardiff's recent poor home form."