The U's dominated the first half and went in front through Jamie Cureton on 34 minutes, but the Bees produced a stirring second-half comeback with goals from Ismail Yakubu and Jason Puncheon.
Colchester's lethal strike partnership of Cureton and Chris Iwelumo had earlier shown why they had scored an impressive 26 goals between them so far this season prior to kick-off.
The big Iwelumo knocked a high ball down for his sidekick in the first minute but Cureton's firm shot was well saved by Lee Harrison.
However, Barnet did not start badly and had a chance of their own on 15 minutes when a Kevin Watson mistake allowed Puncheon to play in Nicky Bailey but U's goalkeeper Dean Gerken got down at his feet to deny him.
It was a missed opportunity they were left to rue on 35 minutes when a Nicky Nicolau slip allowed the clinical Cureton to slam home his 14th goal of the season.
The former Reading striker started to run the show after this and two minutes later his superb cross-field ball released Richard Garcia who blazed over.
Cureton even showed his battling side on the stroke of half-time when a brave header which left him grounded by a defender put Kemal Izzet clean through only to fire straight at Harrison.
Midfielder Izzet then turned provider for Colchester's next chance moments after the break but Kevin McLeod shot wide from a good position.
It gave Barnet the wake-up call they needed and after a goalmouth scramble at the other end, Dean Sinclair rounded the keeper only to see his shot blocked by Chris Barker.
Barry Cogan also had a decent effort from the edge of the box tipped round the post by Gerken in a good spell for the home side.
The Bees were growing in confidence as they searched for an equaliser and ten minutes into the half the lively Bailey shot just wide from 25 yards.
Colchester needed some fresh impetus and brought on Jamie Guy and Johnnie Jackson on 58 minutes. The two linked up almost instantly as Jackson had a goal ruled out for offside.
But Barnet had the momentum and got a deserved equaliser three minutes later through the unlikely source of defender Yakubu.
He found himself clean through after a great forward run, and although his shot hit a defender, it looped over the despairing Gerken into the net.
Colchester threatened to break Barnet hearts when McLeod hit the post 12 minutes from time but it was the men from Essex who went home empty handed.
Puncheon hit a sweet shot from the edge of the box into the top corner ten minutes from time sparking wild scenes at Underhill.