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Rovers had made an early incursion through Ijah Anderson with a free-kick which was swept away by Kevin Sharp.
Scunthorpe were quick to reply forcing two corners in succession but failed to take advantage and then Steve Torpey and Mark Jackson saw efforts go close.
United continued to enjoy most of the play and Matt Sparrow combined well with Paul Hayes, whose shot was just off the mark.
The visitors took the lead after 13 minutes when Robert Quinn's free-kick was knocked into the middle by Kevin Street for Adam Barrett to head home.
The Iron were not dismayed as both Sharp and Nathan Stanton were denied and before the interval Hayes had two further chances but was unable to turn them into anything positive.
United dictated much of the game and were on level terms in the 63rd minute. Anderson tripped Sparrow in the box and Peter Beagrie smashed the ball home with his right foot.
However the game took another twist in the closing stages when Lee Hodges was introduced and he scored what proved to be the winning goal in the 85th minute taking advantage of an error by summer signing Cliff Byrne.
Scunthorpe had two late chances to hit back when young Scottish striker Steven McLean was unlucky to see two classy efforts strike the bar.