Carlton Ubaezuonu scored the only goal of the game in the 39th minute and the away side held onto that lead to earn the three points.
The result meant that the Bulls finished the season in 10th whilst the Iron ended it in second.
Paul Caddis made just the one change to the side that lost to Kidderminster with Sammy Robinson replacing Jaiden White who dropped to the bench.
Andy Butler also made one alteration to the team that beat Peterborough Sports with Ubaezuonu coming in for Danny Whitehall who dropped out of the squad through illness.
The visitors had the first chance of the game in the fifth minute when Callum Roberts made his way into the box, he then played a dangerous ball across goal but Lawson D’Ath was on hand with a crucial last-ditch block.
Hereford grew into the game over the next 20 minutes with plenty of possession and a few set pieces but nothing that troubled Ross Fitzsimons.
Scunthorpe then got back on top and came close in the 26th minute when Tyler Denton nearly scored a wonder goal from range but his effort was just over the bar.
After a quiet period, Butler’s side took the lead in the 39th minute when the Bulls were caught short at the back, Joe Rowley picked the ball up in space and slipped it through to Ubaezuonu who opened up his body and slotted it past Theo Richardson.
On the cusp of half-time, the away side came close again when Rowley was picked out at the back post from a free-kick, he flicked the ball onto the post and it bounced straight into the arms of Richardson which meant that it was 1-0 going into the break.
The Bulls had their first big chance of the game in the 50th minute when Richardson hit a brilliant ball forward which found Omari Sterling-James, he then cut inside onto his favoured right foot and forced a good save out of Fitzsimons.
Caddis’ side kept up the pressure and six minutes later had another opportunity when Remaye Campbell was played in behind but he got his shot all wrong and it went well wide.
Scunthorpe came close to doubling the lead just past the hour mark when the ball was played out to Denton on the left wing but his effort ricocheted off the far post.
After another quiet period, Richardson was forced into a good save in the 75th minute when he palmed a deflected effort from Rowley away.
Hereford pushed for an equaliser late on but could not find one which meant that it finished 1-0.
Hereford FC XI- T. Richardson, K. Coates, M. Preston, K. Howkins, L. Hudson (J. White 61’), T. Campbell, L. D’Ath (A. Babos 68’), S. Robinson, O. Sterling-James (A. Williams 74’), Y. Ceesay, R. Campbell (J. Cowley 74’)
Unused Sub: A. Skinner
Scunthorpe United XI- R. Fitzsimons, M. Kelly, M. Kouogun (A. Boyce 72’), W. Evans, M. Clunan, A. Beestin (M. Brogan 82’), C. Roberts (S. Fishburn 90+7’), J. Rowley, C. Ubaezuonu (K. Scales 72’), J. Starbuck, T. Denton
Unused Sub: M. Fadera
Attendance: 4733 (499 away)