Jamille Matt scored a scrappy 67th-minute winner to lead Alexander's in-form side to a fourth successive victory.
Pompey mustered only one shot on target in the entire 90 minutes as the early-season promotion favourites slumped to their third defeat of the campaign and their third in four home games.
Manager Guy Whittingham said: "We didn't play as well as we have done in the past but I don't think we deserved to lose.
"In the second half for some reason we just couldn't get going and our passing was a bit off.
"They were able to cope with everything we threw at them, have spent a lot of money and have got some very good players.
"Fleetwood have come and stopped us from playing. We never really got going. We didn't move the ball as quickly as we ought to have.
"When we play our bright forward stuff we're a match for anyone, but our tempo was too slow and we didn't lift it, particularly in the second half.
"There were questions whether their goal was offside but the whole goal was scrappy and messy.
"John Sullivan made a great save from Matt and the ball ricocheted in off Bradley's shin."