The home side's opener came from a throw on the right, Jamille Matt getting ahead of the Pompey defence and although his shot was saved by Trevor Carson, Jon Parkin was well placed to stroke home the rebound.
The lead was doubled 10 minutes later. Steven Schumacher crossed the ball and Daniel Alfei was adjudged to have pushed Josh Morris, leaving Antoni Sarcevic to fire his spot kick straight down the middle.
Charlie Taylor could have extended the home side's lead 10 minutes after the break but was denied by Carson after racing clear.
But the respite for Pompey was short-lived. Matt took advantage of confusion in a crowded box to stab home Fleetwood's third after another set-piece.
Pompey were not sunk however, and hit back in spectacular fashion through substitute Wallace, his dazzling run crowned with a stinging shot to end the club's three-game goal drought.
But it was not enough to spark a fightback and Fleetwood substitute Mikael Mandron had a chance to make it four at the death, but fired wide.