Reduced to 10 men after 57 minutes when Chris Clark saw red, the Pilgrims rallied to triumph thanks to Yannick Bolasie's crisp 74th-minute penalty.
Argyle were thrown a lifeline when striker Joe Mason went down under a challenge from Matt Heath and referee Oli Langford awarded a spot-kick. And cash-strapped Argyle - docked 10 points at the beginning of the week - held out to end a turbulent six-day spell with a battling victory.
Peter Reid's side bounced back from Tuesday`s 4-0 thrashing at leaders Brighton with a spirited start, rewarded by Rory Fallon's eighth-minute opener, swept home from close range. Fallon pounced after Colchester failed to clear their lines and Bondz N'Gala headed the ball back towards goal.
Argyle should have gone further ahead before the Us levelled when Nathan Clarke's prodigious throw-in caused confusion in the home penalty area and eventually ended up in the net off Argyle defender Stephane Zubar in the 41st minute.
Kari Arnason almost put Plymouth back in front earlier than they did when he smashed a 25-yard effort off the crossbar at the start of the second half.
Source: PA
Source: PA