Bradley Wright-Phillips gave Southampton the lead in the 52nd minute, but Colchester were level six minutes later.
There was an element of fortune about the goal as Mark Yeates crossed low into the area from the right and the ball was diverted past Southampton goalkeeper Kelvin Davis by the outstretched leg of defender Rudi Skacel.
But both sides had plenty of opportunities to have won the game, showing Southampton's smallest crowd of the season why they were the two highest-scoring teams in the division.
Colchester goalkeeper Aidan Davison was troubled by an early shot from Youssef Safri, while a shot from Jhon Viafara drifted across the face of the goal.
Davison was again busy keeping out a header from Grzegorz Rasiak and from a free-kick by Skacel.
But Colchester had the two best chances of the first half and there was no excuse for Kevin Lisbie as he raced clear in the 42nd minute onto a mistake by Wayne Thomas.
Lisbie had only Davis to beat but dragged his shot wide.
Then, Clive Platt could not reach a pass from Lisbie with the goal at his mercy just before the break.
After the goals there were chances for both sides again, but the best of those fell to Colchester.
Lisbie should have done better in the 63rd minute than lift a shot wastefully over the bar from ten yards after the Southampton defence had failed to clear.
In the 80th minute, Yeates cut in from the right on to his left foot, but from the edge of the area could only drill a low shot straight at the goalkeeper.