Until then a first-half goal from Poland striker Grzegorz Rasiak looked like earning Reading only their second home league win this season.
Reading had far more of the possession in the first half and Scunthorpe had an early escape when Jay Tabb sent Jobi McAnuff clear down the left.
When his cross came over it was stabbed just wide of his own post by Scunthorpe skipper Rob Jones.
As Reading continued to push forward, Raziak sent a header just wide and then completely missed his kick when in with a chance from close range.
Scunthorpe were finding Rasiak hard to handle and he got his head to Ivar Ingimarsson's right-wing cross only to send the ball just over the bar.
Rasiak's persistence was rewarded with a goal after 16 minutes. He climbed above marker Marcus Williams to head home from a pass by Hal Robson-Kanu. It was his sixth goal of the season to make him Reading's leading scorer.
Reading almost grabbed a second straight away with Robson-Kanu setting up Gylfi Sigurdsson for a shot. That was saved by Lillis and, as the ball ran free, David Mirfin just got the ball away for a corner before McAnuff could pounce.
Sigurdsson drew a great save from Lillis in the 35th minute with the keeper, a replacement for the suspended Joe Murphy, diving full length to his right to push the Icelander's free-kick wide of the upright.
When the corner came across, Reading central defender Alex Pearce sent a left-foot effort crashing against the crossbar.
Reading almost stretched their lead early in the second half but Lillis made an instinctive point-blank save for Sigurdsson and was later to make a magnificent save from Rasiak.
Adam Federici came to Reading's rescue when he ran just outside his area to clear from Garry Thompson. The ball ran free to Josh Wright but he lifted his return effort over the bar.
Scunthorpe kept battling away and were rewarded when Josh Wright's pass caused confusion in Reading's defence, allowing Hooper to score.
There was still time for Sigurdsson to hit the Scunthorpe crossbar from a free-kick with three minutes remaining and substitute Jonathan Forte to miss an easy chance for Scunthorpe in injury time.