Jaime Peters' first goal of the season extended Town's unbeaten away run to eight games.
The Canada international levelled the scores just before the hour when he got on the end of Carlos Edwards' pass and buried his shot past Joe Murphy.
Scunthorpe had dominated the first-half and deserved to be up at the break with David Mirfin heading them into the lead on the half hour.
Both sides had clear cut chances to have taken all three points with Peters having a header cleared off the line, Jason Scotland denied from close range while Jonathan Forte fired wide when clean through late on.
Roy Keane reverted to the starting line-up that beat Cardiff in Town's last Championship fixture after making eight changes in the midweek Carling Cup win at Millwall. Jake Livermore started on the bench after joining from Tottenham on loan.
It was Scunthorpe who dominated the first-half though and they could easily have had more to show than Mirfin's solitary goal.
Martyn Woolford sent a free-kick over the bar from 22 yards after Darren O'Dea had brought down Forte inside the first five minutes, then Chris Dagnall fell over when looking to be through on goal.
Grant Leadbitter threw himself in the way of Josh Wright's shot before Forte had a great chance to put the Iron ahead on 15 minutes but the striker couldn't keep his header down from Eddie Nolan's cross.
Woolford dragged his shot wide after Dagnall set him up, then it needed the outstanding Gareth McAuley to clear the danger at full stretch after Dagnall got around the back.
Rob Jones headed wide with Marton Fulop beaten from a corner before Town finally got into Scunthorpe's box midway through the half, Edwards' throw punched clear by Murphy.
It took another timely tackle from McAuley to stop Forte in his tracks inside the Town box, Leadbitter blocking a Wright shot on the edge of the area as Blues struggled to get any foothold in the game.
Cliff Byrne picked up the only yellow card of the game after blocking off Andros Townsend before Scunthorpe got the breakthrough they had threatened on the half hour. Sam Togwell fed the ball back into the box after Blues had cleared a corner and Mirfin beat Fulop with a perfectly directed header.
Blues immediately made a change with Connor Wickham replaced by Luke Hyam, and a switch back to the system that has served Town so well on the travels this season with Jason Scotland operating as the focal point of the attack.
The Trinidad international was only inches away from getting on the end of Edwards' cross as Town began to carry a threat and after a series of corners and long throws into the box, McAuley was denied at the backpost.
Peters replaced Townsend at half-time in Blues' second change and Town started the half a lot more positively, Leadbitter crowded out in the box.
It needed a smart save from Fulop to deny Forte though when the striker escaped down the Town right, Forte then shooting straight at Fulop a minute later.
Blues' equaliser came on 58 minutes, Edwards fed the ball into the box, Bryne's clearance was blocked by Peters and the versatile wideman did the rest superbly.
Town should have been ahead two minutes later, Edwards went through on goal, Murphy made the save, Scotland showed composure to cut inside the defender from the rebound but with the goal beckoning, his shot was forced wide by Byrne's tackle.
Town looked a completely different side from the first-half showing and McAuley threw himself at Leadbitter's corner but couldn't keep his header down.
O'Dea hit the bar after Murphy struggled to deal with Edwards' throw as Blues dictated the play and looked the far more likely to score, David Norris firing just wide.
Leadbitter couldn't get on the end of O'Dea's cross as the game entered the last 20 minutes, Scotland then making way for Tamas Priskin.
Edwards cleared off the line as the Iron threatened from a goalmouth scramble, while Mirkin was alert as Priskin almost got in at the other end.
Peters almost grabbed a second on 78 minutes, his header cleared off the line by Rob Jones, Priskin failing to find the net with a header from the rebound.
Fulop saved low down from Nolan's shot as chances appeared at both ends and it needed a combination of McAuley's brilliant tackle and Fulop's outstretched hand to deny Forte.
Tom Eastman teased a cross just wide, then sent a left footer over before Scunthorpe made their first changes seven minutes from time, Wright and Michael Collins replaced by Andrew Wright and Michael O'Connor.
Tommy Smith powered a header just over but Forte should have won the game at the other end, beating two defenders but sliding the ball the wrong side of the post from 12 yards in the last two minutes.
Scunthorpe: Murphy, Byrne, Jones, Mirfin, Nolan, J.Wright (O'Connor 84), Collins (Grant 84), Togwell, Woolford, Dagnall, Forte. Subs not used: Slocombe, Raynes, A.Wright, Godden, Canavan. Booked: Byrne.
Town: Fulop, Eastman, McAuley, Smith, O'Dea, Edwards, Norris, Leadbitter, Townsend (Peters 46), Scotland (Priskin 73), Wickham (Hyam 31). Subs not used: Murphy, Livermore, Lambe, Kennedy.