Portsmouth lead going into the break against Morecambe after Jake Jervis punished Padraig Amond's penalty miss.
Portsmouth started brightly and went ahead when Jed Wallace's cross from the left was turned in by Jervis.
Morecambe responded well and equalised when Mark Hughes's looping header bounced in off the underside of the bar.
However, they missed the chance to go in front from the penalty spot when Amond's penalty was saved by Portsmouth keeper Trevor Carson.
Jervis then heaped more misery on Morecambe when he tapped home Marcos Painter's ball into the box for his second of the game.