The U's made the trip to Spurs' state-of-the-art training facility at Hotspur Way in Enfield on Tuesday for the behind-closed-doors friendly, with plenty of first-team players featuring for the League Two club.
Colchester ran out 2-1 winners in the game, with loanee Jack Tucker heading them ahead from a set-piece corner and Oscar Thorn bagging the winner.
The likes of Samson Tovide, Tyreece Simpson, Tom Smith and academy starlet Lennox Emery also featured for the U's, in the one-off game.
U's boss Cowley said: “It’s been a really good week for us, really productive.
“At the beginning of the week, we were able to get them some game time.
“They did a lighter session on Monday and they trained Tuesday.
“The boys who I call our finishers and who have been on the periphery of our squad played at Tottenham’s training ground, which is really good.
“We’re thankful to Tottenham for having us and allowing us to play against them.
“We played their 21s and it was a really good workout, a really good game.
“Tottenham play in such an expansive way with the ball and such an aggressive way with the ball, so it was a really challenging game for our boys and we got lots from it.
“We came through that well and we’ve been able to come back together as a group this morning and have started the preparations for MK Dons, on Saturday."
Colchester are hopeful Harry Anderson will be available again for their game at MK Dons.
The winger missed the 1-1 draw with AFC Wimbledon last weekend but has trained fully, this week.
Cowley added: “Harry passed a fitness test on Saturday morning but when we looked at it, we just felt that the risk was too big.
“Particularly in the wide areas, we’ve got lots of competition so it didn’t make sense to risk him but we’re hopeful that he’ll be available, come Saturday."