An early Sam Mantom thunderbolt was cancelled out by a second-half Ryan Edwards header but Luke Williams’ decisive spot kick sent Scunthorpe through.
United made six changes to the team that drew with Oxford United 10 days previously as Joe Anyon, Williams, Paddy Madden, Hakeeb Adelakun, Mantom and Jordan Clarke were all handed a place in the line-up.
It was a lively start to proceedings as Madden charged down the right flank before almost finding Williams with a ball into the centre and then Aaron Wildig’s shot from twelve yards was blocked for the away side.
Scunthorpe didn’t have to wait long for an opener however as Mantom fired high into the roof of the net with just a few minutes on the watch, following a brief spell of pressure.
One almost became two soon after when Adelakun completed a neat control and spin in the area, only to see his fierce drive superbly tipped onto the crossbar and trickle out for a throw-in.
Mantom and Duane Holmes both forced visiting goalkeeper Danijel Nizic into action as the Iron put their opponents under the cosh, which was amplified when Madden stabbed just wide following a swift break forward.
Shrimps ‘keeper Nizic then made another save when Williams played a one-two with Richie Smallwood and struck for goal as United really began to turn up the heat.
There was still time for Graham Alexander’s men to go close once more as the half drew to a close after Adelakun won the ball, beat a series of defenders and saw his eventual cross cleared only as far as Mantom, who headed inches past the post.
The 1-0 lead was certainly no more than Scunthorpe deserved and Morecambe had Nizic to thank for keeping them in it at the midway point.
Veteran winger Kevin Ellison helped spark the visitors into life moments after half-time when first, he dragged wide from 20 yards out before narrowly missing the target with a rebound attempt after Anyon had made a brilliant one-handed stop.
In truth, the Shrimps came out with real vigour ahead of the second forty five and levelled when Edwards rose highest to score after a succession of corners had tested the Iron backline.
United did respond well and threatened to regain the advantage instantly when Williams looped a half-volley wide and substitute Neal Bishop saw a nodded effort cleared off the line.
An attack down the left then resulted in Madden finding Adelakun, who smashed across goal and watched as his shot went just the wrong side of the upright.
Morecambe’s Australian glove man Nizic then pulled off a further save to deny Williams, getting a finger on his powerful hit from distance, and Madden later fired over when well placed in the box.
Clarke and Williams again tried their luck as Scunthorpe continued to pepper the opposition goal before Anyon did well to keep out a low, drilled effort at the other end.
The cup clash finished all square at the end of normal time and so penalties were required to find a winner. United went first and here’s the story of the shootout…
van Veen SCORED
The Iron progressed 5-3 on penalties.
Scunthorpe United: Anyon, Wallace, Williams, Madden, Adelakun, Mantom, Smallwood (van Veen, 82), Holmes (Bishop, 50), Goode, Townsend (Morris, 90), Clarke.
Substitutes not used: Daniels, Wiseman, Hopper, Butroid.
Morecambe: Nizic, McGowan, Edwards, Winnard, Murphy, Ellison (Turner, 72), Conlan (Molyneux, 85), Wildig (Mullin, 79), Whitmore, Stockton, Rose.
Substitutes not used: Roche, Wakefield, Kenyon, Massanka.