A first half own goal and second half strikes from Callum McNally and Michael Ndiweni put Newcastle 3-0 ahead at St James’s Park before Samson Tovide and T’aizo Marcel-Dilaver made the scoreline more respectable for the visitors late on.
The win sees Peter Ramage’s side progress to the fifth round of the competition where they face a trip to Blackpool.
The young Magpies created the first decent opportunity of the match inside the opening two minutes as Ben Parkinson’s cross from the right sailed just wide of the left post.
And after just 12 minutes, the hosts took the lead as Jamie Miley's cross caused havoc for the Colchester defence as they attempted to clear the danger only for the ball to deflect into their own net.
At the other end, Max Thompson had to be alert to deny Samson Tovide equalising straight away.
Tovide thought he’d headed Colchester level after 22 minutes but the offside flag quickly went up as Newcastle’s 1-0 lead remained intact.
An end to end opening 45 minutes unfolded without any big chances opening up for either side until the fourth minute of first half stoppage as Frankie Terry squandered a great opportunity to draw Colchester level. The midfielder scuffed an effort wide of the right post one on one as Newcastle led 1-0 at the break.
Shortly after the restart, Newcastle doubled their lead with a fine low volley from Callum McNally going into the bottom right corner of the goal.
Michael Ndiweni was then alert to make it 3-0 with a fine finish into the bottom left corner of the goal.
It was third time lucky for Tovide in the closing stages as he pounced to pull a goal back for Colchester following a good save from Max Thompson.
Substitute Marcel-Dilaver then set up a nervous end to the game by making it 3-2 in stoppage time.
But Newcastle were able to see the game out to progress after 11 minutes of added time. The only downside to the match was injuries to McNally, Jay Turner-Cooke and Josh Stewart.