The U’s won 2-0 in their final group game against Hayden Mullins’ youngsters thanks to late goals from Samson Tovide and Jack Tucker, at the JobServe Community Stadium.
The win means Colchester won their group, ensuring a home tie in the Round of 32 but they were made to wait for their victory, with Fulham’s outstanding young goalkeeper Alfie McNally making a string of fantastic saves, including a second-half penalty stop to deny Jaden Williams.
U’s boss Cowley said: “Three wins in the competition out of three games, which I think is really pleasing and a clean sheet is really pleasing.
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“To score two goals past their goalkeeper [Alfie McNally] – I’d love to see their number one goalkeeper, if he’s their number two.
“He was Dino Zoff, Edwin van der Sar, probably the best Fulham goalkeeper I can remember – he was all of them tonight, because he was incredible, the amount of saves he made.
“The two saves he made in the first half, one off Will Goodwin and the save from Jaden Williams’ header where he used the depth of his line just to claw it out and then his penalty save in the second half, he was incredible.
“It was going to take a really, really good goal to beat him and thankfully Samson found that.
“We had to stay really patient and we did and a moment of brilliance from Samson ultimately won us the game.”
Breakthrough - Colchester United's Samson Tovide celebrates with Kaion Lisbienull (Image: Steve Brading)
Tovide came off the bench to bag his first Colchester goal since August in some style, with a superb finish into the far corner in the 80th minute.
“It was an exquisite finish from him,” continued Cowley.
“Form is temporary, class is permanent.
“We all know the talent that Samson has and sometimes, nines just need a goal and that will be good for him, for sure.”
Tucker sealed Colchester’s win four minutes after Tovide’s fine strike, heading home from an Arthur Read corner.
Clincher - Jack Tucker heads home Colchester United's second goal (Image: Steve Brading)
Cowley said: “We thought Jack would score from a set piece tonight.
“We worked hard on them yesterday [Monday] and it was a clever set piece.
“A really good corner from Arthur Read and a good header from Jack.”
Colchester came up against a Fulham under-21 side who were missing several players from their normal squad and managed by former U’s head coach, Hayden Mullins.
Cowley added: “Fulham were a really young team.
“I thought they were really well coached, really well organised and a credit to their football club and Hayden Mullins – I thought he did a really good job with them.
“We’ve got a lot of young players at our club and we’re working with them all the time and I know how tiring that can be!
“So for him, with a whole team of them, I thought he’d organised them really well.
“They were very, very difficult to break down; of course, we had a lot of the ball and quite a lot of chances but we had to stay really resilient and thankfully we did and won the game.”