Stevenage's 3-0 victory over Bury saw them seal sixth spot and deny the Magpies a shot at promotion by virtue of goal difference, but Keith Curle's side did their best, with everything they touched turning to goals in the first half.
After Jeff Hughes and Brian Wilson traded inch-wide long-range shots, County took the lead in the 23rd minute when a corner from Alan Sheehan was fired into the six-yard box and Hughes nodded home.
Ten minutes later, Alan Judge drove forward down the left before swinging in a cross that hung up deliciously for Adam Bogdanovic to loop a header past Ben Williams.
The goal of the game came four minutes from the break as Judge cut in from the wing and thumped a dipping shot home from 25 yards.
County would have needed to get into double figures to overtake Stevenage and did their best, Freeman making it four-nil in the 51st minute, passing the ball into the far corner after a neat one-two. Anthony Wordsworth pulled a goal back for Colchester in the final minute with a well-taken finish from the edge of the penalty area.