But full-back Moloney struck the winner with 15 minutes left on the clock for the promotion-chasing Cobblers as Notts suffered just their third defeat at home in League Two this season.
Ricardo Moniz made four changes to the side which lost 2-0 at Salford City in the FA Cup. Izale McLeod's suspension for accumulating five yellow cards allowed Stead a chance to play as the central striker with Genaro Snijders coming in on the wing.
Stanley Aborah and Alan Smith were replaced in central midfield by Curtis Thompson and Gill Swerts, whilst Graham Burke had recovered from injury to take the place of Kyle De Silva.
Notts started well with Burke finding Stead in the channel with a floated pass and the striker got the better of Zander Diamond to pull the ball back for Liam Noble, who scooped his effort over the bar from eight yards out.
At the other end, Nicky Adams' free-kick curled across the six-yard box and through a crowd of bodies with no visiting player able to get a decisive touch to turn the ball home.
It looked as though it was going to be an open game. Noble saw a goalbound shot hit Stead whilst a teasing cross by Adams was headed a yard wide of the post by Cobblers' top-scorer Marc Richards.
Burke saw a rasping effort rise over Adam Smith's crossbar and then had a shot which hit McDonald to go behind for a corner, which was cleared.
The Northampton central defender was then the difference-maker in the Notts penalty area as he rose highest to meet another cross by Adams and plant a header over Roy Carroll, off the underside of the bar and into the back of the net.
County looked to bring themselves level before half-time but Snijders could only smash his shot off the outside of the post after racing onto Stead's flick and Burke hammered an effort into the side-netting from a narrow angle when he could perhaps have passed to Noble, who was screaming for the ball with space inside the box.
Sheehan's flighted pass was collected by Snijders but the winger slid his effort past Smith and across the face of goal with no County player in the vicinity as the Magpies trailed by a solitary goal at the break.
Ronan Murray made his return from a long-term injury at half-time as he replaced Thompson with Notts putting more emphasis on attack in the second period.
Moniz's side started on the front foot - Noble blazed high and wide from 12 yards before the equaliser arrived on 51 minutes.
Noble's knockdown from Sheehan's lofted ball forward fell perfectly for Stead, who smashed hard and low into the corner beyond Smith to bring Notts level with his fifth goal of the season.
Elliott Hewitt blocked a shot from Adams after the winger embarked on a mazy run towards Carroll's goal and goalscorer Stead dragged a shot into Smith's arms as both sides tried to find the goal to give them the lead.
Alfie Potter fired wide from 25 yards before the visiting team regained the advantage as Moloney bundled his way past a couple of players on the edge of the area and arrowed a shot into the bottom corner.
Moniz made a double substitution, bringing on Jimmy Spencer and Adam Campbell to go all-out-attack for the final 10 minutes.
Despite a late scramble in the Northampton goalmouth, the substitutes were unable to make an impact as County's four-game unbeaten run in League Two came to an end.
Notts: Carroll; Hewitt, Edwards, Sheehan, Audel; Swerts, Thompson (Murray, 45), Noble; Snijders (Spencer, 79), Stead, Burke (Campbell, 79).
Subs not used: Loach, Sprockel, Amevor, Smith.
Attendance: 5,513 (999 away)