United looked the more promising side in the opening exchanges and, after Cliff Byrne had headed over from 38th yards, full-back Richard Jackson came to Hereford's rescue with a goal-ine clearance from Izzy Iriekpen.
The former Hereford loanee Gary Hooper spurned a good chance to open the scoring on 15 minutes, intercepting a short Dean Beckwith backpass but seeing goalkeeper Darren Randolph come racing out to block his shot.
After surviving this early pressure, Hereford hit back to take the lead on 25 minutes. Matt Done's run into the Scunthorpe area was cut shot by Iriekpen's crude high challenge and referee Gavin Ward pointed to the spot.
Nick Chadwick took full advantage by blasting home the spot-kick for a debut goal for the home side.
Paul Hayes missed a good chance to respond, heading Byrne's cross over from a great position while Martyn Woolford sent a fierce drive flying high over Randolph's goal.
But eight minutes into the second period a swift break out of defence saw Hayes slip the ball to Sam Togwell, who rifled a shot into the corner of the net.
Hayes was involved again in the second goal with a pass which sent Hooper racing away to drive low past Randolph. Hereford tried desperately hard to hit back and the introduction of substitute Simon Johnson produced a new urgency.
The former Leeds man was unlucky with a curling shot which hit the inside of a post and bounced back into the arms of goalkeeper Joe Murphy.
Johnson was behind another good move which ended with Toumani Diagouraga heading just over.
Scunthorpe held on, however, to the three points to make their long journey home all the sweeter.