Referee Atkinson then incensed the United boss when he awarded the visitors a 78th minute spot-kick when substitute keeper Tomasz Kuszczak was adjudged to have brought down Milan Baros. The United keeper was subsequently red-carded for the offence although Wayne Rooney was almost behind his goalkeeper as the last line of defence.
Rio Ferdinand went in goal but was beaten from the spot kick by Sulley Muntari that gave Pompey victory.
"I think this game was decided when Ronaldo's penalty was refused," Ferguson said after the 1-0 defeat ended United's treble chances.
"I think that gave them great confidence to hang on knowing the referee was on their side and Diarra's had, I don't know, eight-nine fouls in the match, it's incredible.
"I have got to agree with Arsene Wenger that someone's going to get a serious injury in our game. I know that he's had one himself and it's not a nice time to talk about that but the treatment Ronaldo's getting, I'm worried about that.
"But we didn't need to worry about the referee in terms of the chances that we had.
"That guy will go and referee a game next week, no problem."