The Shrimpers threw away a 2-0 lead to allow the U's to take a 3-2 lead, but Portmouth loanee Christophe bundled the ball home five minutes into stoppage time to earn a point.
Blues took the lead in the eighth minute when Dan Harding floated in a free-kick from the right to the far post, where Peter Clarke beat the Farmers keeper Dean Gerken from 15 yards.
And the hosts doubled their advantage in the 13th minute when Lee Sawyer crossed from the right flank, Alex Revell failed to make proper contact but Francis Laurent, starting off as well as Tuesday, slid the ball home from six yards.
The Blues at this point were in total control with Sawyer bossing the midfield and it seemed only a matter of time before they scored a third.
Colchester were struggling to find an opening and saw Dean Hammond hit the sidenetting, before Scott Vernon controlled well but then flashed a shot wide of the left post.
But the visitors reduced the deficit after 35 minutes when Johnnie Jackson's free-kick from 25 yards took a deflection off the five-man wall and beat Adam Federici's dive to the right. A fortunate goal but it got them back in the match at the right time.
The goal lifted Colchester, who saw Mark Yeates denied by Federici before the same player hit the crossbar.
Harding went off to be replaced by Sankofa and once again we started to see the defensive jitters of Bristol. Francis is no left back.
A scrappy second half saw few chances. The best was an early David Perkins' shot from the left which was held at the near post by Federici.
But all that changed when Yeates, the best player on the pitch by the end of the game, equalised for the Farmers on 71 minutes. Perkins' run went unchecked and he passed to Yeates, who rode several tackles before rifling the ball past a diving Federici from just inside the box.
And the U's went ahead in the 81st minute when unmarked substitute Anthony Wordsworth headed John White's centre from the right in at the far post, seven minutes after coming on.
The home side was visibly tiring after their hard match against Leeds, Colchester having had the week off.
However, a sustained last effort, led by substitute McCormack and one which saw keeper Federici go up into the opposition penalty area, finally saw Christophe grab the late equaliser when Kevin Betsy's left-wing corner was nodded on by Clarke and the French midfielder bundled the ball over the line.
Cue wild celebrations for Shrimpers, shocked and despondant Farmers, and pub profits going up all over Southend!
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