The hosts had the bulk of the ball and pressure, coming close when Billy Sharp struck the post from close range.
The game otherwise lacked clear-cut chances, though Cobblers midfielder Matt Taylor saw his long-range free-kick superbly saved by Simon Moore.
With frustration kicking in the ball fell nicely for Freeman, who smashed in from six yards to give United victory.
Blades boss Chris Wilder was facing his old club for the first time since leaving Northampton in May, and has led his new team to four wins in a row.
Rob Page's mid-table side defended valiantly throughout, but have now lost five of their past seven league matches.
Match ends, Sheffield United 1, Northampton Town 0.
Second Half ends, Sheffield United 1, Northampton Town 0.
Substitution, Northampton Town. Joe Iaciofano replaces Sam Hoskins.
Attempt missed. John Fleck (Sheffield United) left footed shot from the centre of the box is too high.
Attempt saved. Caolan Lavery (Sheffield United) left footed shot from outside the box is saved in the bottom left corner.
Goal!  Sheffield United 1, Northampton Town 0. Kieron Freeman (Sheffield United) right footed shot from very close range to the high centre of the goal.
Attempt blocked. Caolan Lavery (Sheffield United) left footed shot from outside the box is blocked.
Corner,  Sheffield United. Conceded by Aaron Phillips.
Substitution, Northampton Town. Harry Beautyman replaces Marc Richards.
Attempt missed. Mark Duffy (Sheffield United) right footed shot from the centre of the box misses to the left.
Corner,  Northampton Town. Conceded by Simon Moore.
Attempt saved. Matthew Taylor (Northampton Town) left footed shot from outside the box is saved in the top left corner.
Foul by Jack O'Connell (Sheffield United).
Alex Revell (Northampton Town) wins a free kick in the defensive half.
Substitution, Sheffield United. Matt Done replaces Daniel Lafferty.
Attempt missed. John Fleck (Sheffield United) left footed shot from outside the box is high and wide to the right.
Stefan Scougall (Sheffield United) wins a free kick in the defensive half.
Foul by David Buchanan (Northampton Town).
Attempt saved. John Fleck (Sheffield United) left footed shot from outside the box is saved in the centre of the goal.
Substitution, Northampton Town. Alfie Potter replaces Paul Anderson.
Foul by John Fleck (Sheffield United).
Alex Revell (Northampton Town) wins a free kick in the defensive half.
Substitution, Sheffield United. Stefan Scougall replaces Chris Basham.
Caolan Lavery (Sheffield United) hits the right post with a header from the centre of the box.
Attempt blocked. Mark Duffy (Sheffield United) right footed shot from the centre of the box is blocked.
Foul by Jack O'Connell (Sheffield United).
Matthew Taylor (Northampton Town) wins a free kick in the attacking half.
Corner,  Sheffield United. Conceded by David Buchanan.
Substitution, Sheffield United. Caolan Lavery replaces Leon Clarke.
Foul by John Fleck (Sheffield United).
Marc Richards (Northampton Town) wins a free kick in the attacking half.
Attempt missed. Leon Clarke (Sheffield United) header from the centre of the box is high and wide to the left.
Foul by Paul Coutts (Sheffield United).
David Buchanan (Northampton Town) wins a free kick on the right wing.
Marc Richards (Northampton Town) wins a free kick on the right wing.
Foul by Ethan Ebanks-Landell (Sheffield United).
Second Half begins Sheffield United 0, Northampton Town 0.
First Half ends, Sheffield United 0, Northampton Town 0.
Attempt missed. Leon Clarke (Sheffield United) header from the centre of the box is close, but misses to the right.
John Fleck (Sheffield United) wins a free kick in the defensive half.
Kieron Freeman's late strike was enough for a patient Sheffield United to beat Northampton and go top of League One.