Chorley, set up by Leon McSweeney, drove a powerful shot into the bottom left-hand corner.
Huddersfield collapsed in the final minutes after Jamie McCombe was sent off for an off-the-ball incident involving George Porter after 84 minutes.
Orient substitute Kevin Lisbie headed in Dean Cox's corner seconds later and from then on it was all Orient. Town's performance went to pieces and it was no surprise when Chorley levelled.
Huddersfield, now unbeaten in 35 league games, were in control until then. Alan Lee headed them in front from Jack Hunt's cross after 22 minutes. Lee Clark's side doubled their lead when Hunt drove in from distance in the 67th minute.
Both sides had goals ruled out for offside - Porter for Orient and substitute Gary Roberts for the hosts. Oscar Gobern hit the crossbar early on for Huddersfield, while Orient were denied a first-half penalty after Antony Kay brought down Porter in the box.