A cross from Gavin Massey found the head of a Stevenage defender but his weak clearance was volleyed into the corner by the in-form Sears.
The U's came out for the second half with attacking intent and Jabo Ibehre put them ahead as he stabbed home following a Chris Day mistake.
Sears made it three with a smart finish from Ibehre's pass and it could have been more as Day denied the U's on another couple of occasions.
A late Freeman free kick made for a nervous finish but the U's held on for three much needed points.
The game started with both sides knowing that it was a vital match in the relegation battle, and neither wanted to make mistakes.
The U’s were looking to stretch the Stevenage defence with balls into the channels for Sears and Ibehre to exploit early on but Chris Day in the home goal was always on the edge of his box and was able to mop up when required.
The first real chance of the game resulted in the first goal, with hosts Stevenage getting the breakthrough.
Doughty’s first touch from Zoko’s pass was heavy but he just managed to nick the ball past Wright and then slip his shot low into the net past Sam Walker.
That came on ten minutes and it provided the only test that either keeper had in the first quarter of the match.
On twenty six minutes, Gavin Massey, Jabo Ibehre and Freddie Sears were all denied by blocks in quick succession, as the U’s looked for the equaliser.
Zoko hit an overhead kick over the bar on thirty one minutes, before Magnus Okounghae blocked a Doughty effort at the edge of the box.
Day hadn’t had a shot to save in the first half but went in at half time beaten, thanks to an injury time strike from Freddie Sears.
Massey crossed to the far post but it was Stevenage defender Obeng who got to it first to head clear.
Fortunately, it was a poor header and Sears calmly guided his volley into the top corner to make it 1-1 at the break.
It was a repeat of the previous week, with the U’s scoring late in the first half, but this time, they continued the momentum at the start of the second.
It was all U’s in the early stages, and it only tool them three minutes to get ahead, with Jabo Ibehre making it nine goals for the season.
Sears put a corner into the near post, Day made a real hash of his punch and Ibehre was quickest to react and poked home from close range in front of a noisy away following.
A long clearance almost set Sears away two minutes later but Day got there first and the resultant ball from Ibehre found Sears in an offside position.
As the U’s continued to dominate, Sears was denied by a near post save from Day, blocked on the edge by good defending and then denied again by a superb point blank save.
Okuonghae headed a corner just over the bar and it was a case of when not if the U’s got a third goal.
It eventually came on seventy two minutes, and it was the ever dangerous Sears who doubled his tally.
Sanchez Watt dispossesses Smith, found Ibehre and after a great turn, the former MK Dons front man moved the ball right into Sears.
Sears touched the ball onto his right foot and drilled his shot low past Day, a slight deflection off the inside of the defender’s leg making no real difference to its trajectory.
It was the buffer that the U’s wanted, and deserved, but a goal from the hosts two minutes from time made it 3-2.
Freeman was fouled on the edge and he stepped up to curl a free kick, deflected on its way past the wall, past Walker and into the net.
There were no further chances at either end but Stevenage finished with ten men as substitute Morias let is frustration get the better of him.
An altercation with Alex Wynter at a throw in led to the dismissal, with Clinton Morrison, on as a sub, booked for his part in the resultant melee.
The whistle went less than a minute later and it was a vital win for the U’s, with four matches remaining.