Shels dangerman Jack Moylan bundled the ball into the back of the Derry net from close range on 66 minutes after a battle with Cameron McJannet, however, match referee Rob Hennessy was well placed and quick to spot a handball by the attacking player.
On a night of controversial referee calls, Duff claimed Moylan denied touching the ball with his hand in the dressing room after the game, adding; 'my players don't lie to me so it's a goal!"
The Dubliners remain on course to clinch European football with games against UCD and Drogheda remaining but it was a frustrating night for Duff and his team on Foyleside.
"When you're playing against 10 men for nearly an hour I guess it's definitely two points that got away," said the former Blackburn and Chelsea winger.
"We dominated the game but after they went down to 10 men did we create a lot? No. But it's certainly two points that got away. We scored a legitimate goal. I guess that's the biggest frustrating thing yet again.
"My players don't lie to me so it's a goal," he continued.
That was the big talking point in the second half and Sadou Diallo's rather harsh sending off was the crucial moment in the match, however, Duff reserved comment on that incident for his counterpart, Higgins.
"Regardless of the sending off in the first half I have absolutely no interest. That's for Ruaidhri to risk a ban. Regarding the goal, it's a legitimate goal. Jack (Moylan), the players, my staff, they're as tight as you get and Jack wouldn't lie to me.
"It didn't look like a handball anyway in real time and I have to say it's an absolutely astonishing, astonishing decision and that's all I'll say on the matter because if I was to comment any more on referees, they're very well protected here. I'll just get a ban and I want to be with my team, my boys, my club on the sideline for the next two weeks. But to be going for Europe and to not be given that goal, is not acceptable."
He certainly hasn't given up hope of qualifying for Europe in his second year in the top flight with fourth spot, occupied by Cup finalists Bohemians, locked in their sights a single point ahead with five points the difference between second placed Derry after Friday's match.
"We still are pushing. We always had plans for the three games, Derry, Drogheda, UCD. We know what we have to do. Are we relying on other results? Yeah, of course. I'm disappointed at the moment but as I said to the players I couldn't have been any prouder, yeah it's a clean sheet which is the least we expected.
"I absolutely demanded off them from 30 minutes onwards when they went down to 10 men that we dominate the game, don't give them any oxygen and don't give them a sniff. And they did that so I couldn't be any prouder of them.
"We're disappointed we didn't get it over the line in the second half but I have to say, hats off to Ruaidhri and his team. Ruaidhri is a brilliant, brilliant man, a brilliant guy and his team defended for their lives in the second half so hats off to them."