David Norris came up trumps with the equaliser in the 88th minute as he was in the right place to steer home a low cross from Sylvan Ebanks-Blake.
Norris' close-range effort cancelled out a 56th minute opener from Kevin Lisbie that looked for a long while like it would be enough to secure a third home win of the season for Colchester.
But the U's have made a habit of conceding late goals and they duly conceded their seventh in the last 10 minutes of the match to keep them entrenched in the lower half of the table.
In fact, they had their keeper Dean Gerken to thank for a number of sensational saves during the final half hour of what was in truth a very drab encounter.
Twice the talented Gerken thwarted substitute Peter Halmosi with wonder saves.
First he turned the Hungarian's long-range free-kick over the bar and just minutes later he parried another goal-bound drive from the impressive midfielder.
Argyle's two front men, Ebanks-Blake and Barry Hayles, endured an evening to forget in front of goal and their misses looked like costing the Devon visitors dear.
Gerken pulled off another smart save when beating away a shot from Norris in the 83rd minute and he was finally beaten from close-range by the same player.
Earlier, Lisbie's opener had come from a similar position. The ex-Charlton man was standing just a few feet from goal as he benefited from keeper Romain Larrieu's failure to hold on to a cracking long-range shot from Mark Yeates.
The alert Lisbie gleefully swept home the rebound to claim his fifth goal of the season since his summer move from Charlton.
Colchester had very few other chances during the game and they can have few complaints.
The U's have only kept one clean sheet in 16 league and cup games and they look destined for a winter of struggle, although their saviour could be their fluency in front of goal at the other end.