The U's finished the season with a defeat, as Notts County won 4-1 at Meadow Lane.
The first half saw the home side open up a three goal gap, with Hughes, Bogdanovic and Judge scoring for the Magpies in a short spell.
Freeman wrapped things up a few minutes into the second half and Anthony Wordsworth's volley at the end was a mere consolation, giving the U's a tenth place finish in League One.
There was one change in the U's starting eleven, with boss John Ward bringing in Karl Duguid for Kayode Odejayi.
The U's Player of the Year limped off with a hamstring injury last weekend and Ward felt it wasn't worth risking him from the start.
He was on the bench though, along with youngster Bradley Hamilton, who made his U's debut seven days previously against Tranmere Rovers.
The home side needed to better Stevenage's result and they had the first attack, Jeff Hughes having a long range shot tipped round the post.
The U's reacted well though, and a minute later were claiming a penalty as Ian Henderson appeared to be held back when a cross came into the box.
Bogdanovic should have shot early in the next home attack but his delay allowed Okuonghae to recover and cover the danger.
At the end of an even first twenty minutes, Brian Wilson got forward to shoot just wide after a cross from the right had been cleared.
A few minutes later though, they were behind as skipper Jeff Hughes rose highest to head home a Sheehan corner.
The goal spurred the U's forward briefly, with Eastman heading straight into Nelson's hands, but it got worse for Ward's men on thirty two minutes.
Alan Judge burst clear on the left and from the goalline, he clipped a cross into the box.
Bogdanovic cleverly placed his header just past the despairing dive of Williams and doubled his side's lead.
It went from bad to worse for the visitors with five minutes remaining, as Judge turned scorer, rifling a long range shot into the top corner.
It gave his side a three goal lead at half time, but as things stood, they would still fail to make the Play-Offs, with Stevenage leading against Bury.
AS the teams came out, Kayode Odejayi entered the fray, coming on for Michael Rose, who had picked up a cut on the top of his foot in the first half.
If the U's were to have any chance of getting back into the game, they had to score the first goal of the second period, and quickly after the restart.
Unfortunately, five minutes in, the home side had increased their lead with a fourth goal.
Full back Freeman burst forward onto a pass, cut inside Okuonghae and hit a low shot into the bottom corner with the outside of his right foot.
That effectively ended the game as a contest, and the home side were looking for blood as they vainly chased the final Play-Off place.
On seventy two minutes, it was almost five, but Williams made a great save with his legs to prevent Judge adding to his and the Magpies total.
With ten minutes remaining, U's skipper Anthony Wordsworth curled a shot straight at Nelson in the home goal.
A minute later, he came closer to a goal but his free kick rebounded off the post and across goal before being cleared.
As the game went into injury time, it was third time lucky for Wordsworth, as his volley from the edge of the box gave the U's a consolation goal.
Seconds later, the final whistle went, on the game and the season, and the U's finished the campaign in tenth place.