The wing-back struck during the closing stages of a match which tested both the patience and perseverance of Chris Wilder's side. Although the goal came via an unlikely source, United did not care a jot. Having begun the contest a point behind Scunthorpe, it moved them into pole position ahead of the meeting between Bolton Wanderers and their rivals from Lincolnshire later this afternoon.
Northampton, now managed by former United defender Robert Page, made a positive start before retreating as the afternoon wore on. Wilder led the visitors to promotion from League Two last term and the competitive streak he instilled in their players clearly still lives on.
Paul Coutts, Mark Duffy and Billy Sharp, the latter during a one-sided second-half, all went close for United.
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But, as Northampton stood firm, only a superb block from Simon Moore prevented Matt Taylor from firing them into a shock lead. It proved a crucial intervention when, with less than two minutes of normal time remaining, Freeman turned home from close range following a low cross from Paul Coutts, arguably the hosts' most impressive player.
Wilder's suspicions that his former club would prove tough opposition proved correct. Indeed, during an action-packed start, both sets of players attempted to grab this fixture by the scruff of the neck. Coutts twice went close early on with shots from the edge of the box while, at the other end of the pitch, his midfield partner John Fleck made a vital interception to deny Sam Hoskins.
United, recalling Leon Clarke to the starting eleven in place of Matt Done, continued to pepper Northampton's box with crosses as Duffy's influence grew. The 31-year-old is a vital cog in Wilder's United machine and, midway through the opening period, saw a free-kick deflected inches wide. It was Duffy's awareness, ignoring calls for him to release the ball quickly, which carved an excellent opportunity for Clarke seven minutes before half-time.
Freeman, charging forward on the overlap, was eventually handed possession and his cross simply begged to be turned home. Instead Clarke, wrestling for position with Lewin Nyatanga, failed to apply the coup-de-grace.
The second period saw United press and probe but, until Freeman pounced, struggle to drag Northampton's defence out of position. Clarke was withdrawn for Lavery as Wilder attempted to change the dynamic of the game. Scougall's introduction proved, beyond all reasonable doubt that United were not prepared to settle for a point.
Sharp saw an overhead kick rebound off a marker during a spell of intense pressure on Adam Smith's goal. But Moore, who had been a bystander since the interval, was called upon to make a wonderful one-handed save when Taylor unleashed an 81st minute free-kick from long-range.
In the 88th minute, United's persistence finally told when Coutts surged forward, Nyatanga tried to clear and Freeman swept the ball into the back of the net. Scougall nearly doubled their lead soon after but Smith denied him with an excellent block.
Sheffield United: Moore, Fleck, O'Connell. Basham (Scougall 69), Sharp, Coutts, Freeman, Ebanks-Landell, Duffy, Lafferty (Done 81), Clarke (Lavery 59). Not used: Ramsdale, Wright, Brown, Reed.
Northampton Town: Smith, Buchanan, Anderson (Potter 69), Zakuani, Richards (Beautyman 86), Revell, Hoskins (Iaciofano 90), Phillips, O'Toole, Nyatanga, Taylor. Not used: Diamond, Gorre, McCourt, Potter, Cornell.
Referee: Darren Drysdale (Lincolnshire). Attendance: 24,194.