The Dragons overturned a 2-1 deficit from the first-leg with a spirited performance that saw them advance to quarterfinals of the elite European competition after 120 minutes of football.
Marega who returned to the European stage after recovering from a thigh injury assisted Tiquinho in breaking the deadlock at the Estadio do Dragao in the 26th minute.
After Dianele De Rossi equalised for Roma minutes later, the 29-year-old restored the hosts lead in the 52nd minute to extend his scoring run in the competition.
Marega has had a hand in eight goals in seven outings in the Champions League this campaign - six goals and two assists.
With the aggregate result tied at 3-3, both teams were forced into extra-time before Alex Telles' effort from the penalty spot in the 117th minute sent Porto to the last-eight stage.