A goal by Paul Osborne in stoppage time following a disputed free kick grabbed the points for Chorley's bogey team Clitheroe.
It followed sustained second-half pressure which had boosted Chorley's hopes of ending a nine-match spell of failing to beat their East Lancashire rivals.
The Magpies took the lead in the 10th minute when Cabbar Bagdagi swept the ball home after keeper James Mann had blocked Adam Farrell's shot but four minutes later visiting skipper Carl Lomax levelled, despite claims for offside.
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Danny Pilkington hit the post with an effort from the edge of the box before Lomax put Clitheroe ahead on 38 minutes with a spectacular drive following a corner.
But two minutes before half-time Mike Eckersley thundered home a powerful equaliser.
Chorley mounted strong pressure in the second half and making use of the flanks looked dangerous in attack.
Eckersley was just wide with a diving header from a Danny Pilkington cross.
The Magpies, who were going for a third back-to-back league victory following wins over Wakefield and Garforth, deserved something from this game.
Jordan Goodeve worked tirelessly in midfield, while skipper Martin Clark turned in another solid performance in defence.
"We were mugged in the last minute," was manager Tony Hesketh's terse summing up.
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