Match official Mark Halsey did award two spot-kicks in Saturday's 2-2 draw, but waved away appeals for two more after Fulham's Emmanuel Frimpong and Philippe Senderos found themselves in the spotlight.
A frustrated O'Neill said: "It looked a pretty clear-cut penalty from Senderos handling the ball, and the referee has chosen not to give it.
"I suppose it sounds like a bit of a moan and a bit of a rant, but last week (in the 2-1 loss to West Brom) there were two penalty incidents in the game and to me, both were penalties given the directives that we have been given by the referees this season.
"One was given against us and the other one wasn't. The referee chose to miss it, and today [Saturday] again.
"While I agree with the referee that, in general, there are a lot of soft penalties being given, these are the directives we have been given.
"While 20 years ago maybe the game would have not had a penalty at all, the fact is that this is not 20 years ago, it's now, and these are the directives we have been given.
"I keep mentioning that point because it was the referees who mentioned it, so you can't just turn around and give it and then choose to ignore it when you want."
It was a game which revolved on a series of debatable penalty decisions, with Mr Halsey enduring a testing afternoon on Wearside.
He pointed to the spot for the first time after 16 minutes when Ashkan Dejagah went down under Craig Gardner's challenge, and Dimitar Berbatov converted in imperious fashion.
Fulham extended their lead 10 minutes before the break when full-back Sascha Riether tapped home after Simon Mignolet had parried Dejagah's shot, but the home side grabbed a lifeline within two minutes.
Mr Halsey ruled that Senderos had tugged Danny Graham's shirt and Gardner smashed home the resulting penalty, setting the stage for Stephane Sessegnon to claim a point 20 minutes from time with the Black Cats turning in a vastly-improved second-half display.
Adam Johnson was convinced his side should have been awarded a second spot-kick when Frimpong appeared to block his shot with an arm, and O'Neill was adamant Mr Halsey should have pointed to the spot once again when the ball bounced up against Senderos's hand seven minutes from time.
O'Neill said: "It was certainly an incident-packed game. We conceded a penalty and then the second goal was, from our own viewpoint, very poor. It was our corner kick and they scored from it.
"But we fought back and I thought we could and should have won the game."
Fulham boss Martin Jol was disappointed his side could not hang on to the lead, but satisfied to emerge with another point for their survival fund.
He said: "Before today [Saturday], if they had beaten us, they would have been on 32 points as well.
"If you look at Southampton, they are in the bottom four or five - if they had beaten QPR today [Saturday], they would have been on 30 points, so everyone can be dragged into a very difficult situation.
"One one hand, it's a good point and on the other hand, three points would have meant we had done the business today [Saturday], but we didn't."
Sunderland winger James McClean, who closed down his Twitter account this week after receiving abuse following a post about an IRA man, was booed by a section of the home fans when he was introduced as a second-half substitute.