Goals from James Bolton and John Marquis saw Pompey progress to the fourth round of the Emirates FA Cup.
They won 2-1 against fellow League One side Fleetwood at Highbury Stadium, with most of the action taking place after the break.
Bolton opened his Blues account from close range following a corner, with Marquis netting in similar fashion soon after.
Cod Army substitute Conor McAleny reduced their deficit in stoppage-time, but it proved no more than a consolation.