Goals in both halves from Luke Williams and then Hakeeb Adelakun sealed the win for the visitors, who progress to the next round with three wins out of three.
There were seven changes to the United side which started against Charlton Athletic previously, alterations that included the return of Williams, who made his first start since August.
The Iron asserted their authority early on and eight minutes in, they created their first chance, as Kevin van Veen fired over following some quick distribution from Joe Anyon.
It would be the hosts who would spurn the game’s first golden opportunity though, with Joe Piggot lifting a shot over from virtually on the goal-line after Josh Coulson had headed the ball back across goal.
Williams, who made such a positive impact from the bench on Saturday, looked to do the same from the off against the U’s. He thought he’d found the net on 15 minutes, but Will Norris did well to block the midfielder’s chip, before Jamie Ness attempted an audacious effort from the edge of the area - which Norris also saved.
Scunthorpe had the ball in the net ten minutes ahead of the interval, when Tom Hopper burst through and neatly finished. The strike was ruled out however, as the forward was adjudged to have fouled his man on the way to scoring.
Moments later though, the Iron did get their deserved breakthrough. Williams’ quick feet were too much for the U’s’ defence to handle, and he rounded off his solo effort with a cool finish over Norris.
A superb block from Murray Wallace preserved the away side’s lead shortly after, as United went in ahead at the break.
That first half lead was very nearly doubled in the early moments of the second, but van Veen sliced his close range left footed strike over the crossbar, following a sublime through ball from Sam Mantom.
Sean Long then came close for the hosts, taking aim from distance. His dipping drive was on target, and swerving, with Anyon doing well to palm the ball to safety.
Anyon had to be alert again when substitute Harry Darling instinctively turned the ball goalwards. The Iron ‘keeper refused to be beaten as he pulled off another top drawer save to keep the score at 1-0.
The chances on the counter were there for Graham Alexander’s side. Adelakun had the next opportunity, cutting in onto his right foot before unleashing a shot which flashed not too far wide of the Cambridge goal.
Anyon was in inspired form and he made it a hat-trick of superb saves with 15 minutes left on the clock. The third of his stops was potentially the best too, with George Maris bearing down on goal. The United stopper was determined to keep his clean sheet in tact though, as he closed down the U’s man.
Full-back Jordan Clarke attempted to wrap the game up in style shortly before the 90 minute mark, but his right footed pile-driver flew over and wide of Norris’ goal.
Williams must have thought he’d got his and the Iron’s second of the night with a well struck effort from the edge of the penalty area not too long after Clarke’s shot. Cambridge ‘keeper Norris spared his own blushes however, as he retrieved his spilled save from the goal-line.
The affair was settled though in injury time by Adelakun, and in some style too. Substitute Jonathon Margetts showed great vision initially to pick out the winger, who lashed the ball low and hard into the opposing corner of the goal.
Adelakun’s finish would prove to be the last meaningful action of the match, with referee Darren Deadman blowing for full time moments later.
Cambridge United: Norris, Adams (Davies, 28), Dunne (Darling, 46), Williamson, Coulson, Long, Dallison, Maris, Clark, Elito, Pigott (Foy, 21).
Substitutes not used: Gregory, Mingoia, Berry, Ikpeazu.
Scunthorpe United: Anyon, Wallace, Williams, van Veen (Smalwood, 82), Hopper (Margetts, 62), Adelakun, Mantom, Goode, Townsend, Ness, Clarke.
Substitutes not used: Daniels, Wiseman, Mirfin, Bishop, Holmes.
Attendance: 666 (86 away).