Deportivo La Coruna striker Pizzi responded almost instantly for the visitors when he buried a spot kick of his own just two minutes later.
Gabon thought they had re-taken the lead before the break when Pepe tried to clear a shot off the line.
After initially awarding the goal the referee consulted his linesman and reversed his decision, much to the annoyance of the home crowd.
Ill discipline came back to haunt Portugal again in the closing stages when Custodio was penalised for blocking a shot with his hand.
Madinda stepped up to convert for the second time and Gabon were able to hold on to claim a famous draw.