Mamady Sidibe struck a brace for the visitors at Meadow Lane as Tony Pulis' men continued their preparation for the top flight.
Stoke took the lead after 10 minutes as Sidibe latched on to a searching through ball to dispatch past goalkeeper Kevin Pilkington.
Just five minutes later, the Malian striker doubled his side's advantage, capitalising on a loose ball in the Magpies' penalty area.
New £5.5million summer signing from Reading Dave Kitson featured in the first 45 minutes for the Potters before being replaced by Jon Parkin in the second half.
Liam Lawrence, Leon Cort, Ricardo Fuller and Dominic Matteo were all missing for Stoke.