At half time, and for much of the second forty-five minutes, the U's held that cherished seventh spot, but Carlisle turned their game around to steal that spot late on in the game.
Tarique Fosu scored both the goals to cap off a strong finish to the season on a personal level, as the U's ended the season with a win.
Colchester finished the season with a 2-0 win over Yeovil Town, but it wasn't quite enough to secure a play off place as the U's missed out by just a point on a dramatic day.
In a cagey first half, Colchester were the better side but it was Yeovil who had the games first chance. Otis Khan was unable to convert just inside the area after his sweeping shot went just over.
The U's first chance came from Matt Briggs as he flicked a header just wide from a Richard Brindley free kick.
It was the same combination six minutes later as Briggs got his head on another Brindley free kick but this time headed straight at John Maddison in the Yeovil goal.
In the 37th minute, Colchester did find the break through and what a goal it was. Fosu took the ball off Chris Porter midway inside the Yeovil half and hit a fantastic 30 yard shot into the bottom corner to give the U's the lead.
This goal seemed to lift both the players and fans with the prospect of a play-off semi final if results stayed as they were after the second half.
There was an extra added edge during the second half as fans eagerly awaited results from elsewhere.
Colchester had a great chance to double their lead through Drey Wright as he was played through on goal by Fosu but Wright blazed over as the ball appeared to bounced just before he shot.
Yeovil then had two half chances themselves, as first Nathan Smith headed straight at Sam Walker from a corner. Then substitute Tom Eaves cut the ball back to Ben Whitfield but he couldn't keep the shot down as the ball went over the bar.
In the 77th minute, Colchester doubled their lead as Fosu scored his second of the game.
A loose ball in the area from a corner dropped for Tom Eastman and his cut back into the area was controlled and finished well by Fosu to give the U's a comfortable lead.
However, the joy of the second goal for Colchester's players and fans was short lived as news filtered through from Exeter's game with Carlisle. With the latter retaking the lead to climb above the U's in the last play off spot.
There wasn't any other action as Colchester controlled the rest of the game and unfortunately for the U's, Exeter were unable to find an equaliser against Carlisle.
This meant that Colchester finished the season in 8th place in Sky Bet League Two and miss out by just a point.
A remarkable achievement by everyone at Colchester in what proved to be a frustrating season with injuries. The U's will now look to build again in the summer and pushed towards promotion.