Missing seven players through injury the home team still started brightly but eventual goalscorer Mooney went in the book after just four minutes when he took a dive in the penalty area following minimal contact from James Chester. The first real chance of the match though coming as late as the 19th minute when Ian Henderson cut in from the left wing for the U's before firing a shot wide of the target.
Carlisle should then have taken the lead only two minutes later when Gary Madine headed a Francois Zoko cross back into the mix for Craig Curran, the United striker though bobbling a poor header wide from close range. Colchester then came back into it with an Anthony Wordsworth free-kick thumped straight into the Blues defensive wall, then on 27 minutes Mooney headed a Brian Wilson ball in bang into the gloves of United goalkeeper Adam Collin.
Mooney though making up for that failure to score two minutes later when this time he sent his header from another Wilson delivery firmly into the back of the Carlisle net. The home side then almost going into the break 2-0 up after 41 minutes when this time it was Mooney who was the provider as his ball into the box found Collin having to make an excellent two-handed diving save to keep out Wordsworth's firm header.
The visitors came out much stronger after the break and early on Tom Taiwo managed to get on the end of a Madine knock down but his shot from the edge of the box disappeared away over the top. Carlisle then going close again after 50 minutes when Madine and McDaid combined to set up Curran for a shooting opportunity that only flew straight at U's stopper Mark Cousins from 18 yards out.
The game got a little end to end now and moments later Wordsworth put Henderson through only for the Colchester man to fire wide, then Zoko's header from a James Berrett corner was easily taken in by Cousins as United once more pressed. Zoko then again in the action as he headed an Ian Harte free-kick over the top before Curran wasted another good chance as he sent his headed effort too high from Zoko's ball in.
United were going at it now and in a busy spell in the game Taiwo had a shot on goal from distance saved by Cousins, before the U's stopper made a fantastic diving stop to keep out Madine's header from a Curran cross. Harte then sent a long range free-kick narrowly wide for the Cumbrians before Kemal Izzet and Berrett entered referee Gavin Ward's notebook as both sides picked up a yellow card apiece.
Carlisle went very close to equalising on 75 minutes when Curran and Taiwo worked together to set up Zoko for a volley that crashed back off the home crossbar, with Cousins then able to collect the rebound. Peter Murphy then hit a shot over for United, with Colchester then having a goal disallowed for offside before the Blues eventually found their late leveller three minutes into injury time when Thirlwell toe-poked a close range finish into the net following a goalmouth scramble.