City's red card woes continued with a fourth red card in five games as Chorley snatched an added time winner at Aggborough.
Sean Geddes' 84th minute second yellow meant that City have now completed just one League game this season with a full team.
Tyler Weir came back into the team to replace Sam Minihan, Rob Elvins made his first start of the season in place of Connor Gater and Ryan Rowe made way for Jamie Spencer.
The early exchanges were fairly even with Sean Geddes shooting from long range for City which was comfortably collected by Chorley keeper Sam Ashton. Clayton McDonald then forced Ashton to punch clear from his header on 6 minutes before Adam Dodd's effort on 9 minutes went just over the bar.
The game continued to go from end to end until Chorley should have opened the scoring on 32 minutes when Stephenson failed to head home Whitham's cross.
Within the space of a minute, City went straight up the other end to open the scoring. Tyler Weir did well to set up Daniel Nit inside the box, his first time effort beating Ashton.
Two minutes later Ellis Deeney shot inches over for City after good work from Nti and Nash on the edge of the box.
On the stroke of half time, the scores were level. Chorley forced a corner which was whipped into the near post by Dale Whitham but Clayton McDonalds attempted header went the wrong way and straight past Nathan Vaughan for an own goal.
The second half saw Chorley take an early lead. Josh Hines cross from the right found Darren Stephenson who turned to finish with a low shot past Vaughan.
Tristian Dunkley came on to replace George Nash and minutes later Danny Jackman replaced Clayton McDonald to make his first appearance of the season.
On 73 minutes Rob Elvins made a double block to deny James Dean and Jake Cottrell before Ryan Rowe came close for City, diverting a Daniel Nti cross narrowly wide.
Sean Geddes shot over the bar from a free kick 35 yards out then Daniel Nti was brought down 25 yards out and an ideal position for Sean Geddes, Nti however, took the ball and smashed it into the top left corner giving Ashton no chance.
With City pushing forward making the best of the momentum, they were once again reduced to 10 men. Sean Geddes, who had been shown a yellow card just minutes before was caught out of position on the half way line, bringing Carver down and giving the referee no option but to give him a second yellow. The loss shook City and Chorley made one last change to try to take all the points with Lewis Guy coming on for Darren Stephenson.
Within a minute the change was to make a difference as Guy's first touch of the game saw him finish from close range to make the score 2-3.
Att: 575