Tony Pulis split his first-team squad for the two games at Lyme Valley and the Weaver Stadium, but neither side covered themselves in glory against their non-league opposition.
A Danzelle St Louis-Hamilton mistake led to Newcastle's opening goal in the seventh minute at Lyme Valley, but Stoke were well on top for much of the first half and at least went into the interval level after Matthew Etherington finished off a smart move in the 37th minute.
Pulis then made six substitutions at half-time but the second half did not go to plan as a mix-up between Louis-Hamilton and Carl Dickinson led to Newcastle grabbing a second goal and an unbelievably rare win over Stoke in the traditional curtain raiser.
The other half of the Potters' squad took on Unibond Premier Division side Nantwich but they fared even worse as goals in either half saw them go down 2-0. Richard Cresswell missed their best chance of the match.
Starting XI v Newcastle: Louis-Hamilton; Wilkinson, Cort, Faye, Dickinson; Soares, Delap, Whelan, Etherington; Beattie, Kitson.
Starting XI v Nantwich: Simonsen; Griffin, Sonko, Shawcross, Higginbotham; Lawrence, Davies, Wedderburn, Pugh; Tonge, Cresswell.