Stephen Hunt's controversial injury-time goal denied Sunderland a point at the Madejski stadium.
Stephen Hunt's injury time winner didn't appear to cross the line
Hunt's shot was clawed away by Craig Gordon but the officials ruled the ball had crossed the line.
Ivar Ingimarsson gave Reading the lead from close range, but Sunderland hit back through Michael Chopra's late penalty after a foul on Kenwyne Jones.
Hunt hit the post as Reading dominated, but Jones missed a great chance for the visitors late on.
Sunderland remain without an away win this season and will feel aggrieved they did not come away with at least a point after clawing their way back into the game.
It's the second time in as many weeks that the Black Cats were left bemoaning a refereeing decision, after they were denied a late winner against Aston Villa last week.
Reading's stoppage time winner will no doubt reignite the debate about the use of goal-line technology as Gordon appeared to have done enough to keep out Hunt's terrific volley.
The majority of the first half was played in Sunderland's half as the home side carved out several chances without finding the back of the net.
But it was the visitors who could have taken the lead in the opening five minutes.
Andy Cole had plenty of time as he escaped the offside trap from old strike partner Dwight Yorke's through ball, but he shot straight at Hahnemann.
The rebound fell kindly for the 36-year-old striker but a bad first touch allowed the Reading goalkeeper to gather at the second attempt.
Dave Kitson's curling effort from the edge of the area went just over, before Gordon dived bravely at the feet of the on-rushing Bobby Convey as the home side began to dominate.
Reading increased the pressure and Gordon kept his side in the game with a brilliant save just before the half hour mark from Hunt's close range header.
Doyle got free in the penalty area but again shot wide as Reading continued to miss chances, before a brief foray into Reading's half saw Chopra shoot high and wide from outside the area.
Ivar Ingimarsson celebrates his opening goal for Reading
With an hour played Hunt, who had been a real handful throughout the game, was denied by the woodwork after cutting in from the right and rifling a left foot shot that crashed against the woodwork.
The game exploded into life in the final quarter of the game with Ingimarsson finally getting the breakthrough for the home side.
Ibrahima Sonko's header from James Harper's free kick was parried by Gordon into the path of the Icelandic defender, who tapped home from six yards.
Doyle missed a great chance to double his side's lead a few minutes later, before Sunderland were given a lifeline ten minutes from time as Jones was brought down in the box by Sonko.
Chopra stepped up to take the penalty and coolly slotted home, sending Hahnemann the wrong way.
Danny Collins forced the Reading goalkeeper into a good save as Sunderland took the initiative, before Jones missed a great chance to put the visitors 2-1 up with two minutes remaining.
It proved to be a costly miss as Reading struck the killer blow deep into injury time as Hunt's volley from Shane Long's cross was adjudged to have crossed the line by the match officials.
Reading manager Steve Coppell:
"I felt we deserved it but I'm bound to say that.
"I would have hoped it would turn out to be one of those emphatic 1-0 wins but as often happens the goal was the signal for the final act in the play.
"And the final act almost turned into a tragedy but in the end was fortunate, which is the best way of putting it."
Sunderland manager Roy Keane:
"Nobody is certain it crossed the line.
"If the referee's assistant can give it then he has got very good eyesight.
"I've seen a replay and I am told to believe every game that if an official is not sure on any decision they can't give it."
Reading: Hahnemann, Murty, Sonko, Ingimarsson, Shorey, Hunt, Harper, Gunnarsson, Convey (Long 84), Doyle, Kitson.
Subs Not Used: Federici, Cisse, Lita, Bikey.
Goals: Ingimarsson 69, Hunt 90.
Sunderland: Gordon, Whitehead, McShane, Higginbotham, Collins, Chopra (Stokes 87), Yorke, Leadbitter, Murphy (Wallace 62), Jones, Cole (Etuhu 62).
Subs Not Used: Ward, Harte.
Booked: Murphy, Leadbitter, Jones, Yorke.
Goals: Chopra 82 pen.
Ref: Steve Tanner (Somerset).
BBC Sport Player Rater man of the match: Reading's Kevin Doyle 8.00 (on 90 minutes).
Please note that you can still give the players marks out of 10 on BBC Sport's Player Rater after the match has finished.