The Young Magpies survived a late scare and 13 minutes of stoppage time to set up a last 16 tie at Blackpool thanks to goals from Callum McNally, Michael Ndiweni and an own goal.
Former Newcastle defender and current under-18s lead Peter Ramage was full of pride following the full-time whistle.
“I'm immensely proud of the players,” he told The Gazette. “They've played at St James's in front of a really good [1,273] crowd and they've got the victory.
"It was backs to the walls stuff in the 13 minutes of injury time but something we're trying to instil in the boys is that resilience to see games out.
"We've been poor in terms of results in the league but on the big occasion they've turned up tonight and got the victory.
"I never had the privilege of scoring at St James's Park but that's something the two lads can take to their grave with them. It's the stuff of dreams for us Geordies and I wish we could have had a couple more but beggars can't be choosers.”
Ramage’s side were dealt a few injury blows during the match as Jay Turner-Cooke, Josh Stewart and McNally all had to be withdrawn.
"We don't know the extent of the injuries yet,” he added. “We've got our fingers and toes and everything else crossed that Callum isn't as bad as we think. “Stewie, we're not 100% sure and probably won't be for the next couple of days but Harry Powell came on and was brilliant.
"He's under-16 and he came on in a pressure cooker situation and he might have done his groin in the build-up to their second goal but they all stood up to see the game out.
“You have to give credit to Colchester as well because they're a really good team with players in and around their first team.
“Their number 9 [Samson Tovide] has been playing for their first team so you can see that because he caused us a lot of problems but we stood up to him and his big threat. We're disappointed to concede the goals we did but we're through to the next round which is the most important thing.”
Following the match, Howe visited the dressing room to congratulate the players along with first team academy graduates Matty and Sean Longstaff.
“[Howe] has been brilliant,” Ramage admitted. “Him coming into the dressing room along with a few of the first team players is brilliant for the lads to see that support from the big boys if you like.
"It was great for me too, speaking to the manager after the game but great for the players to see that as well. He stayed until the end with the players and congratulated them, which is massive for the boys.”