The majority of those inside Fratton Park were cursing referee Carl Boyeson when he pointed to the spot.
He had been alerted by his assistant to an apparent handball inside the Pompey area and awarded Southend a penalty.
Blues players – and supporters – were furious that the decision had been given after Matt Clarke bravely got in the way of a shot.
But the spot-kick was skied into the Fratton End and Brett Pitman went on to score a winner for the hosts.
And despite being frustrated at the time, Danny Rose believes the controversial incident actually worked in their favour.
The midfielder said: “You could tell by our reactions how disappointed we were with the referee’s decision and I think it was very unfair.
“If it’s deemed to be a handball then Clarkey should have been sent off and if it was accidental then it shouldn’t have been a penalty.
"There was a hell of a roar from the crowd when Nile Ranger put it over the bar and I think it was a real turning point."
“He had his hands by his side and the ball was moving at quite a speed. He got his body in the way and that’s what he’s there to do.
“But there was a hell of a roar from the crowd when Nile Ranger put it over the bar and I think it was a real turning point.
“Our tails were up and we knew that we could get something from the game going into the second half.
“Southend set up with the diamond and caused us a few problems when we gave the ball away.
“They passed and probed, but aside from one great save from Luke and the penalty, there weren’t too many chances.”
Rose has started the past two league games for Pompey having endured a lengthy spell out of the side.
He said: “It’s very pleasing to be on the pitch again because you miss being out there with your friends.
“There are not many atmospheres at this level like the one you get here, so you want to experience every moment.
“But every player will have that during the course of their career, so all you can do is keep yourself as fit as possible and believe you can make a difference when you’re next needed.
“The gaffer has been honest with me and the other lads who haven’t been in the team and I’ve just had to remain patient.”