Rio Ferdinand and Jonny Evans are ruled out, but Ferguson hopes Serbian center-back Nemanja Vidic will recover from illness for Wednesday's Champions League trip to Wolfsburg, with United needing a point to finish top of Group B.
United - with only one clean sheet to their name this season - fielded centre-halves Wes Brown and Jonny Evans - in for the injured Nemanja Vidic and Rio Ferdinand - but it was their front men who were the busier pairing.
But Portsmouth hit back seven minutes later with another spotkick, this one more debatable as Nemanja Vidic was ruled to have tugged the shirt of Frederic Piquionne.
Ronaldo, as expected, started on the bench - but Ferguson sprung a surprise by naming Evans in his starting line-up in place of Nemanja Vidic, who is suspended for the meeting with Chelsea.