Spencer came on for Ashley Vincent with 21 minutes left and made his telling contribution 12 minutes later when he hooked in from close range after Grant McCann's corner had been met by the head of Chris Murphy only for his effort to be cleared off the line.
After a forgettable first half, Northampton had stepped up the tempo considerably and grabbed themselves a 63rd minute lead through their top scorer Scott McGleish.
McGleish applied the finishing touch when a cross by Josh Low was played into his path by Martin Smith, McGleish notching his 12th of the season, having also hit the winner on Saturday in the FA Cup against Bury.
McGleish could have added to his tally two minutes later when he turned Jamie Victory inside the penalty area and fired a fierce shot which Shane Higgs could only parry up into the air before retrieving the ball.
At this stage it looked as though the Cobblers would go on and win comfortably with McGleish firing another shot from 25 yards just wide, while Eric Sabin also unleashed a powerful drive which Higgs needed to be at his most alert to keep out.
But the home guard was lowered for Spencer's equaliser and he could even have grabbed an unlikely winner a minute from time when he met a cross from Brian Wilson at the far post, but his free header went wide of the target.
In a dramatic finale home skipper Chris Willmot also hooked a volley over the crossbar.
The first half had far fewer chances although the visitors went close with a flick header by Gavin Caines which forced a scrambling save from Lee Harper, while former Northampton man Jerry Gill made two important stops against his old club, putting in vital foot to prevent Charley Hearn from scoring on his home lead debut.