Alan Pardew's side secured the game in extra-time after Ryan Taylor's second free-kick in as many games levelled the game in normal tie following an early goal by Chris Dagnall
After a slow start that involved more stoppages for free-kicks than anything else, Jimmy Ryan produced the first shot after eight minutes which flew harmlessly over goalkeeper Tim Krul's goal.
Eddie Nolan followed suit and forced Krul into a save as the hosts began to take control of proceedings.
So it was no surprise that Chris Dagnall opened the scoring on 15 minutes, finding the net from close range after work by Michael Nelson.
He looked to add to his tally a few moments later but Krul made save to keep his side in the tie.
The visitors slowly started coming into the game but not before Andy Barcham's attempt which sailed over.
A couple of minutes later Leon Best had Newcastle's fist real attempt at goal, Leon Best shooting following Sylvain Marveux's cross just before the half hour mark which drew a save from Josh Lillis.
The goalkeeper was tested again by Yohan Cabaye but the Magpies couldn't find a breakthrough.
Just after the break Newcastle went close three times in as many minutes - Peter Lovenkrands had a shot saved in between a shot and a header by Best.
The visitors just couldn't get anywhere near the goal as Scunthorpe looked to have held on for a famous victory.
But Ryan Taylor scored his second free-kick in as many games to level the tie with ten minutes remaining of normal time to send the game into extra-time.
The game looked to be going into penalties until Sammy Ameobi- brother of Shola - scored his first competitive goal for the club with a shot from outside the box with eight minutes of extra-time left which was enough to see them avoid being a fifth Premier League side to bow out at this stage this season and saw them through to the next round.