Skipper Andrew Crosby had a superb game; his calm assurance at times was invaluable, while young full back Marcus Williams gave a polished performance in only his second senior outing.
Barnsley were never able to master a solid home side, although Chris Shuker and Paul Hayes were real dangermen.
Stephen McPhail was the key man in the Yorkshire side's defence but they lost the services of big defender Matt Carbon at the interval with breathing problems.
Scunthorpe were first to show when midfielder Ian Baraclough drove a low free-kick in after three minutes, which Nick Colgan saved quite easily.
The Iron might have snatched the lead 11 minutes later, Matthew Sparrow drove the ball in from the right and Steve Torpey should have done better than direct his header wide.
However Barnsley broke the deadlock in the 16th minute when ex-Scunthorpe striker Hayes tucked the ball away after neat work by Shuker, although keeper Paul Musselwhite did get a hand to the ball.
As the game ebbed and flowed it took a fine recovery tackle by Neil Austin in the box to halt a good run by Andy Parton.
Scunthorpe drew level in the 27th minute. Carbon put in a clumsy tackle on Sparrow in the penalty area and Crosby drilled home the spot-kick to Colgan's left-hand side.
Torpey had the ball in the net on the half hour, but he was adjudged to be offside and, as Austin broke through at the other end, Musselwhite was quick to gather the ball.
On the interval Torpey was denied as Colgan turned another fine effort round the post.
Parton, making only his second senior appearance, was denied at the start of the second half when Colgan dived bravely at his feet.
Barnsley looked to have put a second goal on the board when Shuker beat Musselwhite, but Williams stepped in brilliantly to clear the danger.
Scunthorpe shook the visitors when, inside four minutes of arriving as substitute, Cleveland Taylor made a superb run down the right before cutting in to smash home a superb rising shot in the 71st minute.
Scunthorpe continued to look quite dangerous, however, in the closing stages, Barnsley almost snatched an equaliser but Musselwhite was equal to the effort.