Danny Haynes chipped a cross in from the right and Lisbie nipped in between goalkeeper Andy Lonergan and Sean St Ledger to glance a header into the net.
Ipswich dominated early on and both Owen Garvan and Haynes shot wide before Lisbie set up Pablo Counago, but his weak shot was easily held by Lonergan.
The visitors levelled with their first real attack on 21 minutes when skipper Paul McKenna lashed a 25-yarder into the top corner.
Barry Nicholson shot wide from a Neil Mellor pass, before Lisbie blazed wide from a Garvan ball at the other end.
Preston further stunned the home fans when they went ahead on 33 minutes with a clever quick free-kick which saw Billy Jones cross low for Simon Whaley to fire home from close range.
Former England goalkeeper Richard Wright, back at Portman Road after a seven-year absence, dived to save a low Mellor drive, before Lonergan had to be alert to tip away an over hit Nicholson back pass.
Counago fired over seconds after the break as Town looked for an early way back and then Garvan dragged a shot wide when a loose ball fell to him in the box.
Preston got bodies behind the ball and challenged Ipswich to break them down and although Town had plenty of possession, they rarely looked like doing so.
Ipswich did have one or two chances as sub Alan Lee curled a shot just wide and fellow replacement Jordan Rhodes volleyed just over, but ultimately Preston held on with surprising ease.