Sky Blues grab three vital points thanks to Dan Seaborne's first goal for the club in tense encounter at Sixfields
The second new loan signing Nathan Eccleston was named amongst the substitutes.
It was Stevenage had the first chance of the game after four minutes. Curtis Obeng sent a high ball into the box and Francois Zoko sent a looping header towards goal, clipping the outside of Joe Murphy's post and going behind.
The Boro continued to press, after nine minutes Zoko had a shot deflected behind for a corner after some neat passing around the City penalty area.
The game started to develop into a cagey affair, with both sides reluctant to give away possession. City remained strong at the back, playing the offside trap to effect to catch Jordan Burrows after a long through ball found him in space.
Stevenage began to try the high ball though to force an opening. Obeng flashed a volley high over the crossbar after 29 minutes, after a run and cross from Zoko.
With eight minutes of the first half to go, City had their best chance so far. The two forwards linked up and a lovely dummy from Wilson saw Nathan Delfouneso in space, however some last ditch defending blocked his goalbound effort.
The second half started as evenly as the first, however Boro started to enjoy a spell of possession. John Fleck received a booking for a late challenge out wide.
From the resting free kick, a well worked routine saw Jimmy Smith lay the ball to Freeman, whose shot was blocked.
City enjoyed a chance of their own after 58 minutes when Jordan Willis whipped in a cross from the right hand side, but Wilson headed agonisingly over the bar.
Eight minutes later the Sky Blues took the lead. Fleck's delivery from a corner was inch perfect and Seaborne sent a bullet header past Steve Arnold to score his first goal of the season.
Stevenage looked to hit straight back, and started to apply pressure to the City defence. However the Sky Blues soaked up the pressure, as Boro brought on Darius Charles to freshen things up.
City were looking to add to their lead, and on the 78th minute Delfouneso was brought off to hand a debut to Eccleston.
With ten minutes remaining the game was still very much in the balance. Boro had half a chance as Obeng headed from distance but it was gathered safely by Murphy.
As the game entered the final five minutes City were awarded a penalty, as Wilson's goalbound shot was handled by Bira Dembele.
Wilson took the spot kick himself, but Arnold saved low to his left, and his follow up was blocked, denying the striker the chance to score his sixth goal in six games.
Conor Thomas came on for Franck Moussa to help see the game out, but City needed their goalkeeper to produce heroics late on.
In the final minute Joe Murphy produced a stunning reflex save, tipping Zoko's piledriver onto the crossbar when it seemed the ball was destined to go in.
City fans were stunned when six minutes of time were added on by the fourth official, as Stevenage threw everything forward in search for a late equaliser. But it was the Sky Blues who nearly made the game safe, with the tireless Wilson again shooting from 18 yards, the ball squirming but eventually claimed by Arnold.
Boro continued to attack, and with time ticking down Arnold came up for one last corner. But nothing came of it and City held on to clinch a vital three points, and keep Stevenage at the bottom of SkyBet League One.
Attendance: Att 1697 (437 Away)