Swindon again came close to scoring on the half hour mark with a cross from Shakes with both Fallon and Holgate unmarked in the box, but somehow both players missed the cross.
In the second half Swindon still had most of the play with Colchester rarely looking like scoring, but despite coming close Swindon couldn't get any good shots on goal.
Ex Swindon player Mark Yeates came closest to scoring for the Essex side, but his shot was well saved by Rhys Evans in the Swindon goal.
With the game looking like it would finish another 0-0 draw in a row the game reached the 92nd minute with only 1 minute of injury time left before Rory Fallon headed in a close range shot in front of the Town End fans from a Bouazza cross to give Swindon a late and deserved lead.
Overall Swindon had a lot of the play, but few chances in front of goal, so a 1-0 win was a fair and good result. The win still leaves Swindon bottom but they are now only 1 point adrift when a few weeks ago it had been 8 points.
Swindon now go into Wednesday evenings away game to Chesterfield have not been beaten away from home since the start of October, and if they win and other results go their way than Swindon got be out of the relegation zone.