Two second half goals drew Chesterfield level after the Iron had a two goal lead going into half time, meaning a replay is needed to see who will play Derby County in the next round.
On-loan Chelsea defender Alex Davey put the Iron ahead midway through the second half, firing from 20 yards into the top corner.
Lyle Taylor doubled the lead, finishing past Tommy Lee in a one on one minutes before half time.
But Chesterfield came back, Gary Roberts was brought down in the box, Eoin Doyle scored the penalty.
Jay O’Shea levelled the game with six minutes remaining, hitting in at the far post.
Paddy Madden nearly won the game late on, but Lee saved meaning a replay is to decide who progresses.
Iron manager Mark Robins made three changes to the side that triumphed over Rochdale on Boxing Day. Coming into the side was Alex Davey, Sean McAllister and Hakeeb Adelakun, replacing Richard Brindley, Isaiah Osbourne and Liam O’Neil.
On loan Chelsea defender Alex Davey came in for Richard Brindley, with the right-back returning to his parent club Rotherham following the end of his loan spell. Sean McAllister was in the side replacing an ill Isaiah Osbourne. Finally, Hakeeb Adelakun was amongst the starting eleven, taking the place of West Brom loanee Liam O’Neil, who was cup tied for the fixture.
It was a matter of seconds for Scunthorpe to create their first opportunity of the game after a fast paced, positive start to the game. A cross from the right from Alex Davey was floated to the back post, Paddy Madden got up well, but couldn’t keep his header down as it looped over Tommy Lee’s goal.
Neal Bishop was next to come close. An in-swinging freekick from Gary McSheffrey was onto the head of Bishop, who tried to guide it in, but Tommy Lee was equal to it.
Scunthorpe were certainly on top during the opening 15 minutes of the game. McSheffrey and Madden combined in the Chesterfield box, with the latter firing wide from a difficult angle on the left of the penalty area.
Down the other end, League One’s top goal scorer Eoin Doyle was looking to add to his overall tally for the season. He picked up the ball on the edge of the area before firing a dangerous shot towards Sam Slocombe. His shot fizzed narrowly wide of the goal, with Slocombe getting across to ensure his goal was safe.
Armand Gnanduillet too had an opportunity only seconds later, he turned well in the box and got his shot away, but it took a deflection, going out for a corner.
Scunthorpe’s early pressure resulted in them taking the lead with 18 minutes on the clock. A quick attack from the Iron played through Paddy Madden in one on one with the keeper. Lee got down well to save, leading to an Iron corner. From the set-piece, the initial cross was well cleared by Chesterfield, but it was only as far as Alex Davey who waited on the edge of the box. He picked up the ball and fired it into the top corner giving the Iron a well-deserved lead.
Chesterfield had penalty appeals waved away by referee Mark Haywood as Eoin Doyle drove into the box, and was brought down by Miguel Llera. Doyle wanted the penalty but the official deemed Llera to have got the ball, giving a corner instead.
The visitors were piling pressure on the Iron later on in the half, Gnanduillet again going close for Chesterfield, but his header was saved by Slocombe. Romuald Boco too had a chance from the edge of the box, again his volley was claimed by the Iron number one. For a third time Slocombe foiled Chesterfield with minutes left until half time, Gnanduillet hit a shot from inside the area. Slocombe equal to it.
Against the run of play and with little time remaining of the first half, the Iron doubled their lead. A defensive error from Chesterfield allowed Lyle Taylor to take a touch from a long kick up field, compose himself and fire beyond Tommy Lee, who had no chance from the one on one.
After the break, Chesterfield started the brighter of the two sides. Gnanduillet had caused all the problems for the visitors and Sam Slocombe, who was having a wonderful night in front of goal, denied him again. Boco crossed from the right, Gnanduillet won the header and it looked to be going in, but it was well saved.
Chesterfield again came close to halving the deficit. A freekick led to a goalmouth scramble in the Iron penalty area. The ball eventually fell to Sam Clucas on the right of the area. He hit it well, and it looked to be heading to the top corner, but Sam Slocombe was there again to pull off a world class save, keeping Scunthorpe’s two goal lead intact.
The corner count for Chesterfield was into double figures at this point, but the Iron were dealing with everything the visitors were throwing at them. Eddie Nolan was brought on in a defensive midfield role to deal with the Chesterfield pressure.
With 20 minutes left on the clock, Chesterfield were awarded a penalty after Gary Roberts was brought down as he was trying weave some space for himself. Top scorer Eoin Doyle stepped up and fired past Sam Slocombe who had little chance to save the spot kick.
The visitors were throwing everything forward to try and get an equaliser, but the Iron were clearing the danger at any opportunity. Lyle Taylor was trying to hold the ball, relieving the pressure on the defence as they were 10 minutes away from the fourth round tie against Derby. A great run from Marcus Williams nearly allowed the left-back a clear shot on goal, but a good block denied him from putting the home side out of sight.
With six minutes remaining of the match, Chesterfield found an equaliser. They sent the ball forward with Roberts and his cross was drilled across the area. Substitute Jay O’Shea waiting at the back post to blast into the back of the net and level the game.
Sam Slocombe came to the rescue in the dying minutes as Dan Gardner came in with only the keeper to beat, but Slocombe clutched onto the ball well.
Deep into injury time, Madden nearly won it as he burst into the box, but Lee saved well from Madden’s low drive, meaning a replay will decide who will play Derby County in the next round.
Scunthorpe United: Slocombe. Davey (Canavan, 72), Boyce, Llera, M Williams, Bishop, McAllister, Adelakun (Nolan, 60), McSheffrey, Madden, Taylor (Wootton, 78).
Substitutes not used: Weaver, Hawkridge, Myrie-Williams, Mosanya.
Rochdale: Lee, Darikwa, Hird, Morsy, Gnanduillet, Roberts, Clucas, Humphreys (O’Shea, 68), Raglan, Doyle, Boco (Gardner, 68).
Substitutes not used: Wright, Jones, Banks, Talbot, Ariyibi.
Attendance: 4,307 (1,663 away).